Harvest : indels identification
I am looking for insertion and deletion in my dataset with Parsnp and Harvesttools from Harvest. My question is I have SNP information in VCF output file but no indels information. My command is:
Harvest-Linux64-v1.1.2/parsnp -r <reference genome> -d <input dir> -p 32 -o <out dir> -c -x
Harvest-Linux64-v1.1.2/harvesttools -x <xmfa from parsnp> -f <reference genome> \
-n <tree from parsnp> -V <vcf output>
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