User: User000

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User000400
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Posts by User000

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Comment: C: GATK variant calling on multiple bam files
... yeah.... I am not sure this particularity is specified in the GATK documentation... or may be I was not careful enough.. ...
written 18 hours ago by User000400
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Comment: C: GATK variant calling on multiple bam files
... Oh... I realised what was wrong after your answer Pierre.... my bam list file name was bam_list (which works just fine for freebayes and bcftools), but GATK wants bam.list... Now it seems working... a very stupid mistake and all my pipeline was not working for days... :) ...
written 20 hours ago by User000400
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Comment: C: GATK variant calling on multiple bam files
... I checked the header, it is ok, also because when I run all of them a as single bam files all of them work (for now I am working with 5 files to check). I suspect it is not recognizing the list of bam files? ...
written 20 hours ago by User000400
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GATK variant calling on multiple bam files
... Hello, I am trying to do variant calling using GATK on a list of several hundreds of bam files like this: bob.dup.bam smith.dup.bam will.dup.bam This is the command line: java -jar /Tools/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar HaplotypeCaller -L chr1:1-2096 -R ref.fasta -I b ...
gatk bam written 20 hours ago by User000400
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Merging the libraries
... Hello, I have a question regarding merging the BAM files. I have several libraries 4 lanes each. I demultiplexed, mapped against the reference genome, gave the read group name, merged libraries using samtools merge and removed the duplicate reads. Now that I did variant calling I realised I have a ...
readgroupname merge bam written 6 weeks ago by User000400
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Comment: C: Samtools merge BAM files using snakemake
... Seems link is missing :) ...
written 10 weeks ago by User000400
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Comment: C: Samtools merge BAM files using snakemake
... so I just put `-` instead of `_` between the `LIBRARIES` and `SAMPLES` in the output file, so it does not confuse.. seems to be working. ...
written 10 weeks ago by User000400
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Comment: C: Samtools merge BAM files using snakemake
... Actually, the number of libraries match the number of samples, sorry, my bad. Regarding the second part of your answer, could you give more details please? May be a link where I can find more information? Thanks ...
written 10 weeks ago by User000400
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Comment: C: Samtools merge BAM files using snakemake
... Sorry, you are right. I printed a small part of it, should be something like this: ['Bob', 'John', 'Arnold'] ['CL185', 'CL203', 'CL192', 'CL211', 'Cap_2', 'CL472', 'CL236', 'CL269', 'CL222', 'CL216', 'CL65', 'CL235', 'CL350', 'CL306', 'CL442', 'CL430', 'CL201', 'Smith_4', 'CL459', 'CL1 ...
written 10 weeks ago by User000400
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Comment: C: Samtools merge BAM files using snakemake
... They are a lot. Apart from 4 parents which has this format: `Bob_1_Smith_1, Bob_2_Smith_1,Bob_3_Smith_1,Bob_4_Smith_1` I have CL from 1 to 400. I hope this helps, because I do not know if I can post the contents here. ...
written 10 weeks ago by User000400

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