Avatar

registered_user

  • Total activity 23
  • Last activity
  • Member since
  • Following 0 users
  • Followed by 0 users
  • Votes 0
  • Subscriptions 5

Activity overview

Latest activity by registered_user
  • Avatar

    registered_user created a post,

    LeftAlignAndTrimVariants removes header tags

    I noticed that LeftAlignAndTrimVariants (GATK 4.1.8.1) keeps only the first entry of normal- and tumor sample header tags in VCF files. This is unexpected and unwanted behavior. Trimming should not...

  • Avatar

    registered_user commented,

    Thanks for the explanation. For cancer heterogeneity analysis, this is the exact opposite functionality that is required. I think SelectVariants should have some option to remove undetected variant...

  • Avatar

    registered_user commented,

    Nope... this still leaves in variants like: GT:AD:AF:DP:F1R2:F2R1:SB 0/1:52,0:0.019:52:26,0:26,0:35,17,0,0 I think there might be a bug somewhere in Mutect that sets the GT field erroneously to "0/1".

  • Avatar

    registered_user commented,

    Having "##fileformat=VCFv4.2" at the beginning of the --alleles .vcf.gz file seems to have done the trick.

  • Avatar

    registered_user created a post,

    Mutect2 --alleles param GATK_4.1.7.0

    What's going on with the --alleles param for Mutect2? It will not accept a .vcf, .vcf.gz, .list or .intervals file (<chr>:<coordinate>). I have an index for the .vcf.gz file, .vcf.gz.tbi. I am gett...

  • Avatar

    registered_user commented,

    The "-sn" flag is just the short version of "--sample-name".

  • Avatar

    registered_user commented,

    My next idea was to do further filtering based on the AF in the sample data which is "9.123e-03" in the above example row (chr2 70143941)... Looks like SelectVariants adds "AC=1;AF=0.500;AN=2" to ...

  • Avatar

    registered_user commented,

    Looks like the "--remove-unused-alternates" method does not work. I am still getting rows like this in the split sample files: chr2 70143941 . G T . PASS AC=1;AF=0.500;AN=2;AS_FilterStatus=SITE;AS_...

  • Avatar

    registered_user created a post,

    SelectVariants by genotype

    I am trying to separate samples to individual VCF files from a multisample VCF file. What is the correct way to remove rows that are not present in the sample in the resulting VCF with SelectVarian...

  • Avatar

    registered_user commented,

    Took me a while to figure this out, but the GATK list format is actually: <chr>:<start>-<stop>