Question: snp identification with Haplotypecaller and SelectVariants
0
gravatar for felipead66
12 months ago by
felipead6650
felipead6650 wrote:

I want to find the snps for 10 cultivars of almond. Which of the following is correct:

1. Use haplotypecaller to find snps for each cultivar (based on the reference genome), then use selectvariants to find true snps and finally filter the snps with variant filter

or

2.Use haplotypecaller to find snps using as input the bam files for ALL cultivars, then use selectvariants to find true snps and finally filter the snps with variant filter

snp gatk • 360 views
ADD COMMENTlink modified 12 months ago by Pierre Lindenbaum127k • written 12 months ago by felipead6650
1
gravatar for Pierre Lindenbaum
12 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

solution 2 is easier because you'll get all the samples for a given variant. It's easier to filter. If your number of samples is too high you can use g.vcf files: https://gatkforums.broadinstitute.org/gatk/discussion/4017/what-is-a-gvcf-and-how-is-it-different-from-a-regular-vcf

whith solution 1, after merging, you don't know if a missing genotype was HOM_REF or NO_CALL.

ADD COMMENTlink written 12 months ago by Pierre Lindenbaum127k

How to extract gvcf from haplotype caller?

ADD REPLYlink written 12 months ago by felipead6650
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