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Tanay Biswas

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Latest activity by Tanay Biswas
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    Tanay Biswas commented,

    1. Community
    2. General Discussion
    3. GenomicsDBImport-Syntax error in JSON file

    Hi Louis Yeah I saw the warning but I'm not able to understand how to use the argument. Should I just have to add  "--merge-input-intervals true" in my command? Like, gatk GenomicsDBImport -R ~/GRC...

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    Tanay Biswas commented,

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    2. General Discussion
    3. GenomicsDBImport-Syntax error in JSON file

    Hi Louis Each of the vcf.gz file is approx. 4-5 Mb in size. As per my above command, my home directory is filling up. It has a space around 700GB. I have run a new command specifying 256gb memory a...

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    Tanay Biswas created a post,

    GenomicsDBImport-Syntax error in JSON file

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    2. General Discussion

    I'm using gatk to call somatic SNVs and indels. The following error is coming while running GenomicsDBImport to create PON.a) GATK version used: b) Exact command used: java -jar /media/iit/f2bf4ae5...

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    Tanay Biswas created a post,

    Is it necessory to mention disable-read-filter in Mutect2 somatic calling?

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    REQUIRED for all errors and issues: a) GATK version used: gatk-4.3.0.0b) Exact command used: gatk Mutect2 -R ~/hg38.fa -L  ~/S33613271_Covered.bed --germline-resource  ~/somatic-hg38_af-only-gnomad...

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    Tanay Biswas created a post,

    How to specify number of threads while running Mutect2

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    2. Documentation Questions

    REQUIRED for all errors and issues: a) GATK version used: gatk-4.3.0.0b) Exact command used: gatk Mutect2 -R ~/hg38.fa -L  ~/S33613271_Covered.bed --germline-resource  ~/somatic-hg38_af-only-gnomad...

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    Tanay Biswas commented,

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    2. General Discussion
    3. GetPileupSummaries error

    Hi Genevieve Yes. It had the same issue. But I have solved it. Just one thing to ask that If I'm using WES data and I have the h19 covered (target) BED file which I lifted over to hg38, should I us...

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    Tanay Biswas created a post,

    GetPileupSummaries error

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    REQUIRED for all errors and issues: a) GATK version used: b) Exact command used: c) Entire program log: I've hg19 mapped BAM file also. But hg19 gnomad.exome.vcf file is not giving any errors. REQ...

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    Tanay Biswas commented,

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    2. General Discussion
    3. Mutect2 somatic call error

    Hi Genevieve Mutect2 is running and I've understood that why the output file size was different. Thank you.   Regards, Tanay  

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    Tanay Biswas commented,

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    3. Mutect2 somatic call error

    Hi Genevieve Picard was giving error when PU was not mentioned. So I ran the below command: [tbiswas@un02 ~]$ java -jar picard.jar AddOrReplaceReadGroups -I /scratch/tbiswas/IITK-P6-BD_fixmate_sort...

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    Tanay Biswas commented,

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    3. Mutect2 somatic call error

    Hi Genevieve, I have understood the description but I am not able to find anything related to PU. Can you suggest from where should I get the information? Thank you.   Regards, Tanay