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
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?
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')
@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.
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!
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