qslin/huanzhong

Workflow

For Super mutants and SP60/66/132/138

1. Filter SNPs (only homozygous SNPs with good mapping quality and coverage were remained)

sh filter.sh /path/to/snp/file /path/to/genome/reference

2. Compare homozygous SNPs among samples (all common SNPs were deleted)

perl QSBSA.pl -f=/SNPs/to/filter -v=/samples/to/compare -o=prefix

For hvl mutant

1. Filter hvl SNPs, Ler SNPs and hxlf2 SNPs (only SNPs with allele frequency > 50%, good mapping quality and coverage were remained)

sh hvl/filter.sh /path/to/snp/file /path/to/genome/reference

2. Compare SNPs among samples (all common SNPs were deleted)

perl QSBSA.pl -f=hvl/snp3.vcf -v=vcf_all.txt -o=hvl

3. Count hxlf2 homozygous SNPs per 20kb sliding window

perl QSBSA.pl -f=hxlf2/snp4.vcf -m=on -v=off -o=hxlf2