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Forum: Bioinformatics 02-03-2014, 03:23 AM
Replies: 3
Views: 2,016
Posted By mboursnell
Can BLAST handle whole genomes?

Can BLAST handle whole genomes?
Forum: Bioinformatics 02-03-2014, 02:56 AM
Replies: 3
Views: 2,016
Posted By mboursnell
Comparing whole genome sequences

Does anyone know of good software to compare two whole genome mammalian sequences to each other?
Forum: Bioinformatics 12-04-2013, 02:25 AM
Replies: 5
Views: 5,193
Posted By mboursnell
OK, thanks. I'll try exactSNP. How did you do...

OK, thanks. I'll try exactSNP. How did you do the comparison between exactSNP and GATK?
Forum: Bioinformatics 11-29-2013, 05:32 AM
Replies: 5
Views: 5,193
Posted By mboursnell
Question Speed of variant callers

My variant calling seems very slow. What do you think?

We have 10 BAM files, each about 2.5GB, covering a targetted region of about 15MB.

I am using the GATK HaplotypeCaller with 8 threads...
Forum: Bioinformatics 08-02-2013, 12:31 AM
Replies: 12
Views: 6,382
Posted By mboursnell
I think it was the reference sequence in my case....

I think it was the reference sequence in my case. After replacing the file and re-doing the indexes, it seemed to work OK.
Forum: Bioinformatics 11-30-2012, 02:44 AM
Replies: 9
Views: 5,223
Posted By mboursnell
So it seems you don't need to convert before BWA....

So it seems you don't need to convert before BWA. Do you need to convert before GATK or before samtools?
Forum: Bioinformatics 08-31-2012, 03:30 AM
Replies: 0
Views: 3,150
Posted By mboursnell
MarkDuplicates: Value was put into PairInfoMap more than once.

I get this error in MarkDuplicates:

Exception in thread "main" net.sf.picard.PicardException: Value was put into PairInfoMap more than once. 9: WTCHG_29926_01:8:1206:3114:110221#ATCACG


I...
Forum: Bioinformatics 08-29-2012, 06:59 AM
Replies: 5
Views: 2,098
Posted By mboursnell
You're right! I'm sure it used to be required. ...

You're right! I'm sure it used to be required. Maybe that was with UnifiedGenotyper.
Forum: Bioinformatics 08-29-2012, 06:44 AM
Replies: 5
Views: 2,098
Posted By mboursnell
Yes they both are. chrM only once. I...

Yes they both are. chrM only once.

I think now it's down to the the dummy DBSNP file; I don't what to filter any SNPs but it needs file so I have to make a dummy one. Not sure how to make one...
Forum: Bioinformatics 08-29-2012, 03:33 AM
Replies: 5
Views: 2,098
Posted By mboursnell
IndelRealigner ERROR

Whe I run IndelRealigner I get an ERROR like this. It is a whole screen of chrUn something, ending like this:

chrUn_AAEX03026059, chrUn_AAEX03026060, chrUn_AAEX03026061, chrUn_AAEX03026062,...
Forum: Bioinformatics 08-24-2012, 12:23 AM
Replies: 2
Views: 2,061
Posted By mboursnell
EOF error - production of BAM files

These are the commands (with a few of the long paths taken out)

bwa64 aln canfam3.fasta WT22_1.fastq > WT22_1_aln_sa1.sai

bwa64 aln canfam3.fasta WT22_2.fastq > WT22_1_aln_sa2.sai

bwa64...
Forum: Bioinformatics 08-22-2012, 07:19 AM
Replies: 2
Views: 2,061
Posted By mboursnell
Question EOF error in BAM file using canfam3

I have made BAM files using canfam3 as a reference.
Then I am getting this error when using picard/BuildBamIndex

Exception in thread "main" net.sf.samtools.util.RuntimeEOFException: Premature...
Forum: Bioinformatics 08-01-2012, 04:57 AM
Replies: 10
Views: 4,012
Posted By mboursnell
Would it be possible to have a look at your...

Would it be possible to have a look at your Python script to help me setting up my PERL script? mike.boursnell@aht.org.uk
Forum: Bioinformatics 08-01-2012, 03:59 AM
Replies: 10
Views: 4,012
Posted By mboursnell
Do you use the Queue.jar and the...

Do you use the Queue.jar and the DataProcessingPipeline.scala file to run the standard GATK pipeline, or do you make your own pipeline (e.g. in PERL) to do the same thing?
Forum: Bioinformatics 08-01-2012, 03:56 AM
Replies: 10
Views: 4,012
Posted By mboursnell
Thanks. Do I use picard/MergeSamFiles to do the...

Thanks. Do I use picard/MergeSamFiles to do the merging?
Forum: Bioinformatics 08-01-2012, 03:23 AM
Replies: 10
Views: 4,012
Posted By mboursnell
Data Processing Pipeline question

Can anyone suggest an optimum data processing pipeline for analysing dog next gen sequencing data. We start with BAM files, and generally have about 5 cases and 5 controls. (10 samples = 10 BAM...
Forum: Bioinformatics 07-20-2012, 07:26 AM
Replies: 12
Views: 6,382
Posted By mboursnell
Pindel "There are no reads for this bin"

Hi,

I also am having trouble with pindel

I run this command on a BAM file:

/opt/pindel/pindel -f /home/genetics/canfam2/canfam2.fasta -i SHY_01_input.txt -c chr18 -o SHY_01_out

and I...
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