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Documents about ReadBackedPhasing algorithm

YujianYujian Member Posts: 16
edited August 2012 in Ask the GATK team

Hi developers,
Could you share the detailed ReadBackedPhasing algoritm documents with me? As I don't find much more about the algorithm except GATK website, but i have some questions need to read the algorithm carefully and totally understand ReadBackedPhasing.

THanks very much.
Yujian

Best Answer

Answers

  • YujianYujian Member Posts: 16

    if anyone have this material, you could send me email: syjandy@yahoo.cn. Thanks very much~

  • nosaarmannosaarman Member Posts: 1

    I would also be interested in the algorithm. I am hoping to expand this to phase more than 2 haplotypes, or at the very least, I would like to use a similar algorithm to flag exons that contain more than 2 haplotypes.

  • HeidiLingHeidiLing Member Posts: 22
    edited December 2012

    I am playing read backed phasing on one sample and found that all the Het are not phased at all (only Hom are phased which is not informative to me). The sample was sequenced on illumina hiseq 2000 with either 100bpX2 run or 75bpx2. Is this because the setting of cacheWindowSize is not appropriate or I did something wrong. Thanks. below is the commandline I put in.

    java -Xmx4G -jar GenomeAnalysisTK.jar
    -T ReadBackedPhasing
    -R human_g1k_v37.fasta
    -I mysample.bam
    -V mysample.vcf
    -o RBP_mysample.vcf
    -respectPhaseInInput

  • HeidiLingHeidiLing Member Posts: 22

    If I run ReadBackedPhasing after PhaseByTran, there are a few hundred variants (Het) being phased again. But if I run a completely unphased VCF file through ReadBackPhasing, no Het will be phased.

  • ebanksebanks Broad InstituteMember, Broadie, Dev Posts: 692 admin

    That's because you are using the -respectPhaseInInput argument without providing an already phased VCF. Just remove it if you aren't going through PBT first. We'll update the docs to make this more clear.

    Eric Banks, PhD -- Director, Data Sciences and Data Engineering, Broad Institute of Harvard and MIT

  • HeidiLingHeidiLing Member Posts: 22
  • YujianYujian Member Posts: 16
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