Saeed Farajzadeh Valilou
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Recent activity by Saeed Farajzadeh Valilou Sort by recent activity-
Hello, I am trying to get metrics table for a GVCF file using CollectVariantCallingMetrics and I am getting the following error message at the end of run and does not generate metrics table. I was ...
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Hi, I am using the following command for each autosomes and sex chromosome intervals in HaplotypeCaller and I receive memory insufficient error. See the below for the error. Could anyone give a so...
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@Degang I have this line in the header for GenotypeGVCFs: ##GATKCommandLine=<ID=HaplotypeCaller,Version=2014.4-3.3.0-0-ga3711aa, But I am not sure what input has been provided for GenotypeGVCFs ( 1...
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I have a thousand whole-genome sequencing VCF files. Is there any way to figure out and be sure if these VCF files are individually called or jointly called? Is there any line in the header to look...
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Hi, I ran ApplyBQSR, and the size of the WGS CRAM increased from ~15GB to ~50GB. Does ApplyBQSR significantly increase the size of CRAM? Is there any way to maintain the original size of the CRAM? ...
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I'm also have the similar issue. I am working on a similar project, a cohort of ~5,000 human samples of WGS data. I want to perform joint call for all CRAM files. Since, the size of samples are lar...