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Latest activity by registered_user
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    registered_user created a post,

    DRAGMAP and Mutect?

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    1. Community
    2. General Discussion

    I was wondering if the open source DRAGMAP is currently compatible with Mutect? Is it possible to skip the BQSR step if using DRAGMAP instead of bwa-mem in PON creation and somatic variant calling ...

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    registered_user commented,

    1. Community
    2. Other
    3. How to set a COMPRESSION_LEVEL of ApplyBQSR

    Hi Pamela Bretscher, yes I think so. Thanks.

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    registered_user commented,

    1. Community
    2. General Discussion
    3. ApplyBQSR wastes too much disk space

    Solution: gatk --java-options "-Dsamjdk.compression_level=6" ApplyBQSR [options]

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    registered_user commented,

    1. Community
    2. General Discussion
    3. ApplyBQSR wastes too much disk space

    I was able to get a ~25% filesize reduction with running the bam file through samtools view. However, trying to use "ApplyBQSR --java-options "-Dsamjdk.compression_level=6" results in error: Error:...

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    registered_user commented,

    1. Community
    2. General Discussion
    3. ApplyBQSR wastes too much disk space

    This might work:  samtools view -@ 6 -h -b --output-fmt-option level=6 -o compressed.bam uncompressed.bqsr.bam You should be able to leave out "--output-fmt-option level=6" and it should work just ...

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    registered_user created a post,

    ApplyBQSR wastes too much disk space

    1. Community
    2. General Discussion

    I have made the mistake of using the default compression level for ApplyBQSR and now I have terabytes of wasted space in my project bam files. The recalibrated files take up twice the disk space in...

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    registered_user commented,

    1. Community
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    3. How to set a COMPRESSION_LEVEL of ApplyBQSR

    Compression level 2 effectively doubles the file size. I would be interested to know what kind of speed advantage are we talking about here to outweigh this massive waste of disk space. The BQSR pr...

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    registered_user created a post,

    LeftAlignAndTrimVariants removes header tags

    1. Community
    2. Somatic

    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...

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    registered_user commented,

    1. Community
    2. General Discussion
    3. SelectVariants by genotype

    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...

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    registered_user commented,

    1. Community
    2. General Discussion
    3. SelectVariants by genotype

    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".

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