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Old 04-27-2011, 10:40 AM   #1
land_NGS
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Location: California

Join Date: Apr 2011
Posts: 2
Default Dindel empty variant result file

I'm running dindel's first stage analysis set to: getCIGARindels
The run looks good (number of reads read is reported some indels are found, Reports "Done"), but the variant result file as well as the library file are empty.

An idea how to fix this?

Many thanks!

The command, files, run log and output are listed below.





The command I'm running is:
dindel --analysis getCIGARindels --doDiploid --bamFile ERR024149_1_sorted.bam --outputFile out --ref chr20.fa

The directory I set up has 4 files:
-rw-r--r-- 1 root root 63684691 Apr 27 09:58 chr20.fa
-rw-r--r-- 1 root root 23 Apr 27 09:58 chr20.fa.fai
-rw-r--r-- 1 root root 799889680 Apr 27 10:01 ERR024149_1_sorted.bam
-rw-r--r-- 1 root root 6432448 Apr 27 10:01 ERR024149_1_sorted.bam.bai

The run messages are:
Reading BAM file: ERR024149_1_sorted.bam
Parsing indels from CIGAR strings...
Wrote indels in CIGARS for target chr10 to file out
Wrote indels in CIGARS for target chr11 to file out
Number of reads read: 1000000
Wrote indels in CIGARS for target chr12 to file out
Wrote indels in CIGARS for target chr13 to file out
Wrote indels in CIGARS for target chr14 to file out
Number of reads read: 2000000
Wrote indels in CIGARS for target chr15 to file out
Wrote indels in CIGARS for target chr16 to file out
Wrote indels in CIGARS for target chr17 to file out
Number of reads read: 3000000
Wrote indels in CIGARS for target chr18 to file out
Wrote indels in CIGARS for target chr19 to file out
Wrote indels in CIGARS for target chr1 to file out
Number of reads read: 4000000
Wrote indels in CIGARS for target chr20 to file out
Wrote indels in CIGARS for target chr21 to file out
Wrote indels in CIGARS for target chr22 to file out
Wrote indels in CIGARS for target chr22_h2_hap1 to file out
Number of reads read: 5000000
Wrote indels in CIGARS for target chr2 to file out
Wrote indels in CIGARS for target chr3 to file out
Number of reads read: 6000000
Wrote indels in CIGARS for target chr4 to file out
Number of reads read: 7000000
Wrote indels in CIGARS for target chr5 to file out
Wrote indels in CIGARS for target chr5_h2_hap1 to file out
Wrote indels in CIGARS for target chr6_cox_hap1 to file out
Wrote indels in CIGARS for target chr6 to file out
Wrote indels in CIGARS for target chr6_qbl_hap2 to file out
Number of reads read: 8000000
Wrote indels in CIGARS for target chr7 to file out
Wrote indels in CIGARS for target chr8 to file out
Number of reads read: 9000000
Wrote indels in CIGARS for target chr9 to file out
Wrote indels in CIGARS for target chrM to file out
Wrote indels in CIGARS for target chrX to file out
Wrote indels in CIGARS for target chrY to file out
Wrote library insert sizes to out.libraries.txt
done!


The output files are :
-rw-r--r-- 1 root root 0 Apr 27 10:11 ERR024149_1.dindel_output.libraries.txt
-rw-r--r-- 1 root root 0 Apr 27 10:11 ERR024149_1.dindel_output.variants.txt
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Old 04-28-2011, 12:48 AM   #2
gaffa
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Location: Gothenburg/Uppsala, Sweden

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Posts: 82
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You shouldn't use the "--doDiploid" flag at this stage, that's for the realignment step. Not sure if that's the problem here though.
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Old 04-28-2011, 11:16 AM   #3
land_NGS
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Location: California

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You are right. I've added this flag after running without it (according to manual directions) and getting an empty variant file. It does not help to take the --doDiploid flag off.
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Old 09-25-2013, 01:57 PM   #4
Jane Flora
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Location: Ireland

Join Date: Aug 2012
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I am having the same problem of getting empty variant file from dindel. Any suggestions?
Thanks in advance
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dindel, indel, re-sequencing, variation analysis, wgs

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