Is there any way for haplotype calling from Bam files?

30 August 2016 1 6K Report

I wonder if anyone could tell me if it is possible to define the haplotype associated with certain mutation using Bam files and if this is possible which software I can use and the reliability if I want to prove a founder effect in a set of patients, if this makes any sense?

Fred Zhou

Some tips:

1. If small cohort and very small windows, using GATK haplotypecaller with -bamOut to get the read info.

2. If relative large cohort with relative large searching window, use SNP calling software (GATK or others) to generate VCF files, then goes to the variant phasing using phasing software (beagle/mach2/thunder)..

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