jigold / zcall Goto Github PK
View Code? Open in Web Editor NEWA Rare Variant Caller for Array-based Genotyping
A Rare Variant Caller for Array-based Genotyping
Arguments are passed to dropSamplesFromReport.py through sys.argv:
report = sys.argv[1]
dropSamples = sys.argv[2]
However, next section expects use of the usual OptionParser approach used in the other scripts:
if options.report.find(".gz") != -1:
file = gzip.open(options.report)
else:
file = open(options.report,'r')
Hi, first of all amazing project.
Could you please advise how to convert zcall output .tped and .tfam files, in the format of A,B alleles back to vcf format in 0/1 format. I tried the plink commands with --recode vcf, but didn't work as expected. Any advise is highly appreciated. Thanks in advance!
@jigold great project. I am wondering where 'example.bpm.csv' shown in your example inputs folder is produced from? Is it an export from genomestudio or a product of autoconvert? Oddly enough I have produced this file on my own with my own data but can't recall how I did it.
When findMeanSD.py is executed, it creates a file which only contains a header but no additional lines. To make things more confusing, there are no errors given so I don't know what went wrong.
What is a possible cause for this?
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