The current GATK version is 3.6-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
Register now for the upcoming GATK Best Practices workshop, Nov 7-8 at the Broad in Cambridge, MA. Open to all comers! More info and signup at

Documents about ReadBackedPhasing algorithm

YujianYujian Posts: 6Member
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.

Best Answer


  • YujianYujian Posts: 6Member

    if anyone have this material, you could send me email: Thanks very much~

  • nosaarmannosaarman Posts: 1Member

    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 Posts: 22Member
    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

  • HeidiLingHeidiLing Posts: 22Member

    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 InstitutePosts: 698Member, Administrator, Broadie, Moderator, Dev 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 Posts: 22Member


  • YujianYujian Posts: 6Member


Sign In or Register to comment.