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phasing SNPs with 3 siblings

I have SNP data from 3 siblings but no data from parents (not yet). Is it possible to phase the SNPs?

My vcf looks something like this:

1       359     .       G       A       3784.37         PASS            AC=19;AF=0.198;AN=96 GT:AD:DP:GQ:PL:PP               0/0:26,0:26:68:0,65,498:0,68,510                  0/1:9,9:18:99:147,0,92:144,0,101                   0/1:24,28:52:99:488,0,262:485,0,271

So basically, genotypes for 3 individuals (siblings).

chr    pos  ref   alt s1    s2    s3
1      359  G     A   0/0   0/1   0/1
variant-calling snp
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by firestar firestar

Added a snp sample line from the vcf.

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written by firestar firestar

1 answer

there is a tool in GATK 3 named ReadBackedPhasing that use the BAM to phase the variants but I cannot find the doc in the new GATK4.

https://software.broadinstitute.org/gatk/search?q=ReadBackedPhasing

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written by Pierre Lindenbaum Pierre Lindenbaum

I am aware of this. It is not a separate step anymore because it has been incorporated into HaplotypeCaller.

But, I am not sure if it's working very well for me. I think it adds PGT (phased genotype) and PID (phase ID) to the FORMAT field. Very few of my variants have this PGT/PID values. I think it only gives me short stretches of phasing. For example if I take one sample and count how many phased GTs are present, I get 57 in the first 1000 SNPs. Just as an example.

If I understand ReadBackedPhasing correctly, it's based on the fact that variants on one read is evidence that they come from the same chromosome. But with 150bp illumina reads, there is only so far you can get even taking paired-end reads into account.

I was wondering given 3 siblings, if there was a program that would impute the phase information using markov chains or whatever.

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written by firestar firestar

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