Question: snp identification with Haplotypecaller and SelectVariants
0
gravatar for felipead66
8 weeks ago by
felipead6630
felipead6630 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 • 124 views
ADD COMMENTlink modified 8 weeks ago by Pierre Lindenbaum120k • written 8 weeks ago by felipead6630
1
gravatar for Pierre Lindenbaum
8 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k 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 8 weeks ago by Pierre Lindenbaum120k

How to extract gvcf from haplotype caller?

ADD REPLYlink written 7 weeks ago by felipead6630
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