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vibansal / ancestry

program to estimate admixture coefficients from individual genotype or sequence data
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remove prefix "chr" from "chrom" property for reads in bam file #12

Closed wenjiany closed 4 years ago

wenjiany commented 4 years ago

Sometimes bam files were aligned to assembly with chromsome names including string "chr", e.g. "chr1", "chr2", etc. This create mismatch with default chromosomes in current program, expecting 1, 2, etc.

vibansal commented 4 years ago

Program has an option to address this, please see the NOTES:

If your chromosome names have the 'chr' prefix, use the command line option "--addchr=True" for the runancestry.py script