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ReadBackedPhasing

AswathyNAswathyN BangaloreMember

Hello,
I perform variant calling on Amplicon Based Targeted Exome sequencing on Human.
I use a licenced version of GATK (V2014.3-3.2.2-7-g f9cba99).
I am using ReadBackedPhasing for obtaining the Phasing information.
After a successful run of the above tool, it displays that Sites phased are 41. (Screenshot attached)
However, in the output file I don't see any variant with a phased genotype.
The ReadBackedPhasing specific arguments provided are as given below:

java -jar ~/software_stack/GenomeAnalysisTK/GenomeAnalysisTK.jar -T ReadBackedPhasing -R ~/reference_stack/reference/human.fasta -I ~/dummydir/out.bam -V ~/dummydir/Sample.vcf -o ~/dummydir/Sample_Phased.vcf

I would also like to know what would be the ideal horizontal as well as vertical coverage (as per the interval file) for Amplicon based Targeted Exome sequencing to carry out a successful Genotype phasing.

Thanks & Regards,
Aswathy

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin
    edited August 2015

    @AswathyN
    Hi Aswathy,

    Can you please post the bam file and VCF record of a site you think should be phased?

    Thanks,
    Sheila

  • AswathyNAswathyN BangaloreMember

    Hello Sheila,
    I read from a blog that ReadBackedPhasing performs phasing on the vcf data and it is denoted with a tag "HP" instead of "|".
    My output file has "HP" tags for the phased variants. This answered my concerns. But I have a few more questions.
    1) I would also like to know what would be the ideal horizontal as well as vertical coverage (as per the interval file) for Amplicon based Targeted Exome sequencing to carry out a successful Genotype phasing.
    2) Could you please explain what the number in the "HP" field of GT field signifies?
    For your reference a variant record is provided below.

    1 45797508 . C G 1420.54 PASS AC=1;AF=0.224;AN=2;BaseQRankSum=0.550;ClippingRankSum=0.358;DP=316;FS=9.916;GQ_MEAN=29.59;GQ_STDDEV=27.12;InbreedingCoeff=0.0166;MLEAC=14;MLEAF=0.241;MQ=60.00;MQ0=0;MQRankSum=0.406;NCC=8;POSITIVE_TRAIN_SITE;QD=18.21;ReadPosRankSum=0.00;VQSLOD=1.93;culprit=FS GT:AD:DP:GQ:HP:PL 0/1:11,6:17:94:45797505-1,45797505-2:94,0,229

    Thanks,
    Aswathy

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin
  • AswathyNAswathyN BangaloreMember

    Thank you Sheila.. I got the answer..

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