Avatar

Saeed Farajzadeh Valilou

Follow
  • Total activity 26
  • Last activity
  • Member since
  • Following 1 user
  • Followed by 0 users
  • Votes 5
  • Subscriptions 13

Activity overview

Latest activity by Saeed Farajzadeh Valilou
  • Avatar

    Saeed Farajzadeh Valilou created a post,

    How to convert a VCF to GATK VCF Format

    1. Community
    2. General Discussion

    I have downloaded dbsnp v.156 vcf file from dbsnp ftp link and I want to convert it to GATK VCF format. And also I want to change chromosome notations (i.e. 'NC_000001.11' to 'chr1'). How can I do ...

    • Saeed Farajzadeh Valilou
    • 2 followers
    • 1 comment
    • 0 votes
  • Avatar

    Saeed Farajzadeh Valilou commented,

    1. Tool Index
    2. 4.0.1.2
    3. CollectVariantCallingMetrics (Picard)

    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 ...

    • View comment
    • Saeed Farajzadeh Valilou
    • 2 votes
  • Avatar

    Saeed Farajzadeh Valilou commented,

    1. Technical Documentation
    2. Glossary
    3. GATK4 command-line syntax

    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...

    • View comment
    • Saeed Farajzadeh Valilou
    • Edited
    • 0 votes
  • Avatar

    Saeed Farajzadeh Valilou commented,

    1. Technical Documentation
    2. Algorithms
    3. The logic of joint calling for germline short variants

    @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...

    • View comment
    • Saeed Farajzadeh Valilou
    • Edited
    • 0 votes
  • Avatar

    Saeed Farajzadeh Valilou commented,

    1. Technical Documentation
    2. Algorithms
    3. The logic of joint calling for germline short variants

    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...

    • View comment
    • Saeed Farajzadeh Valilou
    • 0 votes
  • Avatar

    Saeed Farajzadeh Valilou commented,

    1. Tool Index
    2. 4.1.6.0
    3. ApplyBQSR

    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? ...

    • View comment
    • Saeed Farajzadeh Valilou
    • 0 votes
  • Avatar

    Saeed Farajzadeh Valilou created a post,

    How to Split 3000 WGS CRAM files into 1Mbp length chunks

    1. Community
    2. Documentation Questions

    Hello, I have 3000 WGS CRAM files and I want to split them into 1Mbp chunks. I want to split with exact genomic coordinate locations, e.g. starting from 1 to 1000000bp, 1000001bp to 2000000bp, 2000...

    • Saeed Farajzadeh Valilou
    • 2 followers
    • 1 comment
    • 0 votes
  • Avatar

    Saeed Farajzadeh Valilou commented,

    1. Community
    2. Germline
    3. Joint Call WGS with a Large Cohort

    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...

    • View comment
    • Saeed Farajzadeh Valilou
    • 0 votes