Is there anaway to see the actual haplotypes (chain of alleles) for a region of DNA using haplotypecaller? I don't want to call genotype (the stage after haplotype construction)
You could use the bamout option to do this. More for info: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_haplotypecaller_HaplotypeCaller.php#--bam-output
I used this bamout flag and color alignment by HC , still i couldn't figure out what the actual parental /maternal sequence is. For example for a region of DNA we have AAT[C/T]GGT[A/T]CC (2 positions are het) then 2 haplotypes could be AATCGGTACC and AATTTGGTTCC. I am wondering if there is any way to produce such an output using Haplotypecaller.
So the bamout option of HC will give you all possible haplotypes created by HC for variant calling. If you want the phasing information (i.e. parental /maternal sequence), that is different from the haplotypes created by HC bamout, and that information will be available in the final vcf created by latest GATK4.1 version of HC.
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Thanks , it worked.