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bmvdgeijn / WASP

WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery
Apache License 2.0
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find_intersecting_snps.py input files #81

Closed Liying1996 closed 5 years ago

Liying1996 commented 5 years ago

Hi! We have some questions about the mapping step 3 (find_intersecting_snps.py):

  1. If we only have unphased files, should we only use the snp_dir/ as the input file rather than h5 files (snp_index.h5, snp_tab.h5, haplotype.h5)?
  2. If 98% snps in a genotype vcf file were phased, is it correct to just use the h5 files as input files?
  3. In snp_dir, all snps are considered rather than only heterozygous snps ? Thank you very much !