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MQ0Fraction, HWP, Dels Tags for VCF file (How to generate)

wlwtanwlwtan SingaporeMember

Hi,

My issue might be very fundamental. I am looking for the values for the tags mentioned in the title after running variantAnnotator on the VCF file. However, they were mentioned in the header section but not included elsewhere. I need these tags for variant filtering.

This is the code that I have used:
GATK=GATK/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar
REF=hg19/hg19.fa

java -Xmx6g -jar $GATK -R $REF -T VariantAnnotator -V h3_variant.vcf -o VA_h3_variant.vcf -A HardyWeinberg -A HomopolymerRun -A MappingQualityZero -A SpanningDeletions

There is no error/warning given.

I wonder if there are any alternatives to these statistics?
Thank you.

Wilson

Answers

  • valentinvalentin Cambridge, MAMember, Dev ✭✭
    edited October 2016

    MQ0 cannot be annotated without the input reads, thus it must be done by HaplotypeGenotyper or UnifiedGenotyper. VariantAnnotator cannot do the job.

    This is also the case with 'Dels'.

    In contrast 'HW' depends only on the genotype calls and so in theory you only need the input vcf. However it seems that HW won't be calculated at all unless the input file contains 10+ samples. Also, at each variant, at least one of those 10+ sample must have a called genotype (i.e. GT != ./.), GQ is present and a value of 10 or above, otherwise HW won't be calculated at that position.

    Does you vcf have at least 10 samples and does it have called GT and GQ annotations?

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @wlwtan
    Hi Wilson,

    I second Valentin's @valentin response. However, I should point out you can indeed input BAM files to VariantAnnotator. If you input the BAM files, you should get HomopolymerRun, MappingQualityZero, and SpanningDeletions. However, as Valentin said, you will not get HardyWeinberg unless you have ten or more founder samples in your VCF.

    -Sheila

  • valentinvalentin Cambridge, MAMember, Dev ✭✭

    Thanks for the correction @Sheila

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