bcftools call with -T only works with .vcf.gz; not bcf

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

678 stars 240 forks source link

bcftools call with -T only works with .vcf.gz; not bcf #120

Open danielecook opened 10 years ago

danielecook commented 10 years ago

Here is what I am running:

samtools mpileup -t DP,DV,DP4,SP -g -f ../reference/ce10/ce10.fa -r chrI JU2464.bam | bcftools call -T ../individual_bcf/complete_variant_set.bcf --format-fields GQ,GP -c -v > ../group_bcf/raw.JU2464.chrI.group.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
Segmentation fault

Results in a segmentation fault.

pd3 commented 10 years ago

-T is not supposed to work with BCF, but you are right, it should not segfault. I will mark this issue as a feature request.

jmarshall commented 8 years ago

This should be retested… possibly has been fixed along the way.

mcshane commented 8 years ago

The segfault is indeed gone, replaced by the error message "Failed to read the targets: complete_variant_set.bcf". Leaving issue open with the enhancement label to perhaps support bcf targets files in the future. Or at least print a more helpful error message.