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Best way to extract SNPs and INDEL from multiple samples

Hi, I am processing multiple samples using the GATK4 haplotypecaller, could you please let me know what would be best way to merge these VCF files and extract the SNPs and INDEL followed by hard filtering separately for SNPs and INDEL. Should I filter each vcf file for SNPs and INDEL and then generate the combined vcf file using the GenomicsDB or can I merge all samples together first using GenomicsDB and then filter the SNPs and INDEL.

gwas wgs ngs
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written by ngseq • ngseq

1 answer

1) use GenomicsDB is to generated VCF from GVCF files (GenotypeGVCFs)

2) filter each VCF chunck by type and hard filter using GATK SelectVariants

3) merge all the filtered chuncks using GatherVcfs

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks Pierre. this is all sorted.

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written by ngseq • ngseq

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