Entering edit mode
10.1 years ago
low.weiquan
•
0
Hi,
I am currently carrrying out a SNP calling pipeline and I have forward and reverse read files that used bwa for alignment and then using samtools mpileup to get the contigs in the form of vcf file. I then proceeded to find the consensus sequence by using GATK FastaAlternateReferenceMaker. How do I check which contigs are used in forming the consensus sequence and even the order?
