Incorrect number of QSS fields (2)

samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

http://samtools.github.io/bcftools/

Other

650 stars 240 forks source link

Incorrect number of QSS fields (2) #834

Closed DadongZ closed 6 years ago

DadongZ commented 6 years ago

I got an error messageIncorrect number of QSS fields (2) at 1:3681211, cannot merge. when I was running the bcftools merge:

bcftools merge --file-list vcffilelist.txt \
    --force-samples \
    --apply-filters PASS \
    --output /data1/workspace/DCI/Kirsch/Yvonne.Mowery/RNASeq-WES/WES/neoantigen/MAF/tmp/Lee-WES_2018.vcf \
    --regions-file /data1/Staging/S0276129_Padded-mm9tomm10-NoChr.bed\
    --output-type v \
    --threads 4

Any suggestions?

pd3 commented 6 years ago

Just added some hints how to troubleshoot this here http://samtools.github.io/bcftools/howtos/FAQ.html. Please reopen if this does not solve the issue.

DadongZ commented 6 years ago

@pd3 I am not able to fix the issue following the instructions in your link.

DadongZ commented 6 years ago

@pd3 why you closed the issue without being solved? I can't reopen it.

pd3 commented 6 years ago

Sorry, it looks a problem with your VCF, not bcftools, that's why I closed the issue. If you think this is a bcftools bug, you'll need to provide more information.