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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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fixvcfmissinggenotypes.jar does not actually fix missing genotypes #198

Closed Giuseppe1995 closed 2 years ago

Giuseppe1995 commented 2 years ago

Hi, I am running, on a merged vcf - let's call it "merged.vcf.gz" (it has also an index) - the fixvcfmissinggenotypes.jar java script as follows

java -jar fixvcfmissinggenotypes.jar --bams bam.list -d 8 --output fixed.merged.vcf merged.vcf.gz

It goes with no error or warnings, but it gives me a file ("fixed.merged.vcf") with the same missingness of the "merged.vcf.gz" (basically are the same file).

Note that to rule out that this could be due to the low coverage of bams I run the command above but with the option -d 1, but it resulted in no different outcome.

Thank you in advance, peppe

lindenb commented 2 years ago

thank you for this report. Please, give me a valid vcf file with only one variant and one subset of bam file overlapping that variant.

Giuseppe1995 commented 2 years ago

Oh, apparently the name of the chromosomes are different in bam and in vcf (bam=chrN,; vcf=N), so this was the problem. I'm sorry have bothered you with such stupid question, but I assumed that there was no discrepancy on the chromosome nomenclature between the two files (this is a dataset I downloaded, sorry again). Thank you for your help!