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pileupCaller only outputing missing data in genofile #26

Closed mscbig closed 2 years ago

mscbig commented 2 years ago

Despite having checked carefully the format of my input files, all sites appear as missing data. Here is an example I grepped for one variable site. In file positions 1 131606

samtools mpileup -R -B -l positions -f ref.fa sample_A.bam > pileup.txt In file pileup.txt 1 131606 T 2 .. JJ

In file eigenpos rs3983 1 0 131606 G T

pileupCaller --sampleNames A -f eigenpos -o EigenStrat -e sampleA.out < pileup.txt

In file samplesA.out.geno.txt 9 In file samplesA.out.snp.txt 1_131606 1 0 131606 G T

When outputing in Freqsum format, consistently produce missing data too

CHROM POS REF ALT A(1)

1 131606 G T -1

Did I miss something obvious in formatting that causes this behaviour?

Thanks

stschiff commented 2 years ago

You've closed this, so can I assume you've solved the issue yourself?

mscbig commented 2 years ago

Yes sorry. I installed the latest version on my personal computer and thanks to the error message it generated I realized it's a problem of chromosome names that causes an error as the pileup file seems unordered.

stschiff commented 2 years ago

Ah OK. Good luck then :-)