Will Pitchers

icon indicating a website link biomebank.com icon indicating an email [email protected]

icon company BiomeBank icon location Thebarton, SA icon location European evolutionary biologist, turned Bioinformatician at @BiomeB ...formerly @MDU-PHL , formerly at @msuefishlab , and @DworkinLab

Results 2 comments of Will Pitchers

output VCF of SNPs

There's some oddness going on with the `sim.vcf` file that TTR outputs: Each row *after* the header rows seems to be broken by an extra line break between the `ALT`...

output VCF of SNPs

Found it! lines 915:916 in `treetoreads.py`: ```python fi.write('''{chrm}\t{loc}\t.\t{refbase}\t{altbase} \t40\tPASS\t.\tGT\t{vars}\n'''.format(chrm=contig_name, ``` ...should be on a single line like this: ```python fi.write('''{chrm}\t{loc}\t.\t{refbase}\t{altbase}\t40\tPASS\t.\tGT\t{vars}\n'''.format(chrm=contig_name, ``` This renders the `sim.vcf` output into a valid `..vcf`-shape...