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  • #61
    Hi kai,

    I met a problem when I run pindel.

    this is the command line:
    pindel -f ../ref/hs_ref_GRCh37.p2.all.fa -i config.txt -c all -o pindeloutput -T 8

    this is the configure file:
    A1.sort.bam 300 A1
    A2.sort.bam 300 A2
    A3.sort.bam 300 A3

    the bam files were generated by BWA, I also try the unsorted bam file, not work too.

    this is the prompt:
    Pindel version 0.2.4o, March 9 2012.
    Processing chromosome: gi|224589800|ref|NC_000001.10|
    Skipping chromosome: gi|224589800|ref|NC_000001.10|
    Processing chromosome: gi|224589811|ref|NC_000002.11|
    Skipping chromosome: gi|224589811|ref|NC_000002.11|
    Processing chromosome: gi|224589815|ref|NC_000003.11|
    Skipping chromosome: gi|224589815|ref|NC_000003.11|
    .............
    Processing chromosome: gi|224514683|ref|NT_167243.1|
    Skipping chromosome: gi|224514683|ref|NT_167243.1|
    Processing chromosome: gi|251831106|ref|NC_012920.1|
    Skipping chromosome: gi|251831106|ref|NC_012920.1|
    Loading genome sequences and reads: 0 seconds.
    Mining, Sorting and output results: 0 seconds.

    could you help me to solve this problem?

    Regards

    Yongbiao

    Comment


    • #62
      Originally posted by Yong-Biao Zhang View Post
      Hi kai,

      I met a problem when I run pindel.

      this is the command line:
      pindel -f ../ref/hs_ref_GRCh37.p2.all.fa -i config.txt -c all -o pindeloutput -T 8

      this is the configure file:
      A1.sort.bam 300 A1
      A2.sort.bam 300 A2
      A3.sort.bam 300 A3

      the bam files were generated by BWA, I also try the unsorted bam file, not work too.

      this is the prompt:
      Pindel version 0.2.4o, March 9 2012.
      Processing chromosome: gi|224589800|ref|NC_000001.10|
      Skipping chromosome: gi|224589800|ref|NC_000001.10|
      Processing chromosome: gi|224589811|ref|NC_000002.11|
      Skipping chromosome: gi|224589811|ref|NC_000002.11|
      Processing chromosome: gi|224589815|ref|NC_000003.11|
      Skipping chromosome: gi|224589815|ref|NC_000003.11|
      .............
      Processing chromosome: gi|224514683|ref|NT_167243.1|
      Skipping chromosome: gi|224514683|ref|NT_167243.1|
      Processing chromosome: gi|251831106|ref|NC_012920.1|
      Skipping chromosome: gi|251831106|ref|NC_012920.1|
      Loading genome sequences and reads: 0 seconds.
      Mining, Sorting and output results: 0 seconds.

      could you help me to solve this problem?

      Regards

      Yongbiao
      Please use "-c ALL", not "-c all". Also make sure that you use the same reference file here you used for mapping. "chr1" is different than "1".

      Comment


      • #63
        Hi Kai,

        I had a few questions I was hoping you could address. Could you provide a bit of information about how incorporating BreakDancer output affects Pindel. I am trying to compare results of Pindel with and without using BreakDancer output as an option. Does BreakDancer make Pindel results more reliable somehow?


        Additionally, I am curious about the 'insert size' for each sample included in the pindel config file. Previously I was just putting 200 as I have 100bp PE data, but this seems incorrect. A more accurate number might be the average size of my library prep (minus the adapter size), which is a bit different for each sample. Is fragment size recommended instead? How will that improve the results?

        Thank you very much.
        Last edited by bwubb; 03-28-2012, 09:24 AM.

        Comment


        • #64
          Originally posted by KaiYe View Post
          Please use "-c ALL", not "-c all". Also make sure that you use the same reference file here you used for mapping. "chr1" is different than "1".
          Hi Kai

          Thanks for you help.

          One more question, there is a column named "The number of reads supporting the SV", but I can not find the total number of reads cover the SV per sample, unless I check this by samtools -tview. I just want to know the confidence of the SVs in the output files. Is there a parameter to reflect this?

          Thanks.
          Last edited by Yong-Biao Zhang; 04-04-2012, 10:03 PM.

          Comment


          • #65
            Originally posted by Yong-Biao Zhang View Post
            Hi Kai

            Thanks for you help.

            One more question, there is a column named "The number of reads supporting the SV", but I can not find the total number of reads cover the SV per sample, unless I check this by samtools -tview. I just want to know the confidence of the SVs in the output files. Is there a parameter to reflect this?

            Thanks.
            As Pindel ignores reads supporting the reference allele to speed up, we only report the number of variant supporting reads per sample with strand and uniqueness information. You may use the two score S1 and SUM_MS to do filterings.

            Comment


            • #66
              Originally posted by KaiYe View Post
              As Pindel ignores reads supporting the reference allele to speed up, we only report the number of variant supporting reads per sample with strand and uniqueness information. You may use the two score S1 and SUM_MS to do filterings.
              Hi Kai

              Thanks for you reply.
              Another question, in the output file of large insertion, it seems that there were no columns of S1 and SUM_MS, as welll as the length of large insertion. Did I make a mistake in manipulating pindel?
              By the way, to get a proper confidence of SV, what cutoff value shoud I set to filter the results?

              Thanks
              Last edited by Yong-Biao Zhang; 04-05-2012, 12:52 AM.

              Comment


              • #67
                Hi Kai,

                I have incorporated pindel into my pipeline, but I have a query about where best to place it.

                Can I run pindel with the realigned.bam files from GATK? Or is it better to run it before this step?

                Thanks,

                Alex

                Comment


                • #68
                  Originally posted by d12ajd View Post
                  Hi Kai,

                  I have incorporated pindel into my pipeline, but I have a query about where best to place it.

                  Can I run pindel with the realigned.bam files from GATK? Or is it better to run it before this step?

                  Thanks,

                  Alex
                  Both are fine but do it after realignment may be better.

                  Kai

                  Comment


                  • #69
                    d12ajd: I think after realignment will be better. I have seen following deletions marked as independent with the same starting position in pindel:
                    A-TTTTTC and
                    ATTT-TTC
                    So, you will loose this deletions as they will have low score hits/total.

                    Comment


                    • #70
                      Thanks for your responses! I will run with the realigned files, Alex

                      Comment


                      • #71
                        KaiYe: Does pindel accept breakdancer files?

                        I tried to use this command: pindel --fasta "human_g1k_v37_decoy_optimized.fasta" \
                        --config-file "config_1" \
                        --output-prefix "$PREFIX-$CHROM" \
                        --chromosome $CHROM \
                        --number_of_threads 10 \
                        --max_range_index 5 \
                        --report_inversions --report_duplications --report_long_insertions --report_breakpoints --report_close_mapped_reads \
                        --min_NT_size 50 \
                        --min_inversion_size 50 \
                        --min_num_matched_bases 30 \
                        --additional_mismatch 1 \
                        --min_perfect_match_around_BP 3 \
                        --sequencing_error_rate 0.03 \
                        --maximum_allowed_mismatch_rate 0.1 \
                        --anchor_quality 20 \
                        --balance_cutoff 100 \
                        --window_size 300 \
                        --minimum_support_for_event 3 \
                        --genotyping \
                        --breakdancer "file_1190575.txt" \
                        --output_of_breakdancer_events "breakdancer-events-$CHROM.txt" \
                        --name_of_logfile $CHROM.log

                        But I didn't get neither breakdancer-events neither log file. Does this options work?

                        Comment


                        • #72
                          Pindel empty output

                          Hi Kai

                          I posted this on a separated thread already, but my problem is that I keep getting output like this:

                          *** Calling SV using Split-Read Analysis: /home/usr/apps/pindel024s/src ***
                          >> Running Pindel on ALL: /home/usr/apps/pindel024s/src/pindel -f /srv/gs1/projects/lab/usr/data/hg19/ucsc.hg19.fasta -i /srv/gs1/projects/lab/usr/dir.2/JS2.sra.cfg -o /srv/gs1/projects/lab/usr/dir.2/JS2.sra -c ALL
                          Pindel version 0.2.4s, June 18 2012.
                          Looping over all chromosomes.
                          Processing chromosome: chrM
                          Chromosome Size: 16571
                          NumBoxes: 60020 BoxSize: 667

                          Looking at chromosome chrM bases 0 to 10000000.
                          getReads chrM 20016571
                          Insertsize in bamreads: 195
                          Number of reads in current window: 0, + 0 - 0
                          Number of reads where the close end could be mapped: 0, + 0 - 0
                          Percentage of reads which could be mapped: + 0.00% - 0.00%

                          No currentState.Reads for chrM found in /srv/gs1/projects/lab/usr/dir.2/JS2_L1_1_pf_aa.sorted.recal.bam
                          BAM file index 0 0
                          There are no reads for this bin.


                          And the configuration file looks like this:

                          /srv/gs1/projects/lab/usr/dir.2/JS2_L1_1_pf_aa.sorted.recal.bam 195 JS2


                          I originally used an older version and then reinstalled the latest version of pindel (0.2.4s) and I get the same problem, the "BAM file index 0 0" "no reads in this bin" for every bin for every chromosome.

                          The only thing I can think of is that maybe something went wrong at the compilation stage of pindel? When i compiled pindel I saw a few errors:

                          /pindel024s> make SAMTOOLS=/home/usr/apps/samtools-0.1.14
                          Created Makefile.local, please review the configuration
                          make: *** No rule to make target `Makefile.local', needed by `pindel'. Stop.
                          scg2:~/apps/pindel024s> make SAMTOOLS=/home/usr/apps/samtools-0.1.14
                          make -C src pindel
                          make[1]: Entering directory `/home/usr/apps/pindel024s/src'
                          make[1]: Leaving directory `/home/usr/apps/pindel024s/src'
                          make[1]: Entering directory `/home/usr/apps/pindel024s/src'
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 pindel.cpp -o pindel.o
                          pindel.cpp: In function 'int main(int, char**)':
                          pindel.cpp:1196:38: warning: variable 'Time_Mine_E' set but not used [-Wunused-but-set-variable]
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 reader.cpp -o reader.o
                          reader.cpp: In function 'int fetch_func_RP(const bam1_t*, void*)':
                          reader.cpp:770:24: warning: variable 'b1_core' set but not used [-Wunused-but-set-variable]
                          reader.cpp:772:18: warning: variable 'b2_core' set but not used [-Wunused-but-set-variable]
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 reporter.cpp -o reporter.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 searcher.cpp -o searcher.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 parameter.cpp -o parameter.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 refreader.cpp -o refreader.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 control_state.cpp -o control_state.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 search_deletions_nt.cpp -o search_deletions_nt.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 search_inversions.cpp -o search_inversions.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 search_inversions_nt.cpp -o search_inversions_nt.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 bam2depth.cpp -o bam2depth.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 search_tandem_duplications.cpp -o search_tandem_duplications.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 search_tandem_duplications_nt.cpp -o search_tandem_duplications_nt.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 output_sorter.cpp -o output_sorter.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 farend_searcher.cpp -o farend_searcher.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 search_variant.cpp -o search_variant.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 searchshortinsertions.cpp -o searchshortinsertions.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 searchdeletions.cpp -o searchdeletions.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 output_file_data.cpp -o output_file_data.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 bddata.cpp -o bddata.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 shifted_vector.cpp -o shifted_vector.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 read_buffer.cpp -o read_buffer.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 assembly.cpp -o assembly.o
                          assembly.cpp: In function 'void TryLI(const std::vector<Chromosome>&, std::map<std::basic_string<char>, int>&, ControlState&, ParCollection&, const Assembly&, std::vector<SPLIT_READ>&, std::vector<SPLIT_READ>&, std:fstream&)':
                          assembly.cpp:606:24: warning: variable 'SecondLength' set but not used [-Wunused-but-set-variable]
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 genotyping.cpp -o genotyping.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 line_reader.cpp -o line_reader.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 ifstream_line_reader.cpp -o ifstream_line_reader.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 gz_line_reader.cpp -o gz_line_reader.o
                          g++ -Wall -g -c -O3 -fopenmp -I/home/usr/apps/samtools-0.1.14 pindel_read_reader.cpp -o pindel_read_reader.o
                          g++ pindel.o reader.o reporter.o searcher.o parameter.o refreader.o control_state.o search_deletions_nt.o search_inversions.o search_inversions_nt.o bam2depth.o search_tandem_duplications.o search_tandem_duplications_nt.o output_sorter.o farend_searcher.o search_variant.o searchshortinsertions.o searchdeletions.o output_file_data.o bddata.o shifted_vector.o read_buffer.o assembly.o genotyping.o line_reader.o ifstream_line_reader.o gz_line_reader.o pindel_read_reader.o -O3 -fopenmp -lm -lz -L/home/usr/apps/samtools-0.1.14 -lbam -o pindel
                          make[1]: Leaving directory `/home/usr/apps/pindel024s/src'

                          (the reason I'm using samtools 0.1.14 is because the pipeline I'm installing was set up with this version and the indexed bam was created using this version. I also tried installing pindel and compiling with samtools 0.1.18 and then running it, but it did not solve my problems and I ended up with the same output...)

                          Any help/solutions you can offer would be greatly appreciated!

                          Comment


                          • #73
                            Can I request a max supporting samples option for the pindel2vcf program? I did not see that as an option in the --help and for my purposes, I want to filter out any SV that occurs in more then 2 samples.

                            Or am I missing how to do this? Thank you.

                            Comment


                            • #74
                              What is SVTYPE RPL?

                              Comment


                              • #75
                                Segmentation fault still exits

                                Originally posted by KaiYe View Post
                                Hi Max,

                                Yes, we also noticed this bug. Please try our latest source code 0.2.4o, updated on March 9 2012.

                                Please do contact us if you experience the same or other issues.

                                Thanks,

                                Kai
                                Hi I am using now pindel 0.2.4t version and also get this message

                                This is my command:
                                Code:
                                pindel -f ../../../genomes/Mus_musculus.chromosome.MT.500add.fa -i bwa_n0.002mismatches.txt -c ALL -o MT_indel -x 9 -s
                                and here is the config file
                                Code:
                                >bwa.sam$ cat bwa_n0.002mismatches.txt
                                A.sam.bam.sorted.bam       300     A_run32_CGATGT
                                B.sam.bam.sorted.bam       300     B_run32_TGACCA
                                C.sam.bam.sorted.bam       300     C_run32_ACAGTG
                                D.sam.bam.sorted.bam       300     D_run32_GCCAAT
                                E.sam.bam.sorted.bam       300     E_run32_CAGATC
                                F.sam.bam.sorted.bam       300     F_run32_CTTGTA
                                G.sam.bam.sorted.bam       300     G_run32_AGTCAA
                                I also tried to run it with the mentioned version 0.2.4o but it gave me the same error message.

                                any ideas to the source of this problem?

                                Thanks
                                Assa

                                Comment

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