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registered_user

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Latest activity by registered_user
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    registered_user commented,

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

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    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...

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    registered_user commented,

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

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    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 ...

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    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_...

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    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...

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    registered_user commented,

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

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    registered_user commented,

    @David_Benjamin, I sent you an email regarding our data, we would be happy for you to take a look at it.

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    registered_user commented,

    I'm noticing the AS_SB_TABLE contains the information I'm interested in. AS_FilterStatus=strand_bias;AS_SB_TABLE=67,35|1,4; where "1,4" tells me the split between the strands. I think I'm going to ...

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    registered_user commented,

    I am experimenting with --pcr-slippage-rate to see how it affects the results. About the orientation bias filtering... I would like to see how the results look if I could specify that a single supp...