question about bcftools merge

[giror]

Hi all,

I was hoping this is the right place to ask this, but if not please let me know.

I am trying to merge 3 *.vcf.gz files using bcftools merge. Two of the files are from our local sequencing center and contain one genome each, and the other one is a vcf of 17 genomes (previously published) from Sanger.

When I call: bcftools merge g1.vcf.gz g2.vcf.gz sang.vcf.gz
I get: *** glibc detected *** bcftools: realloc(): invalid next size: 0x0000000003369fe0 ***

If I then split the genomes by chromosome and call: bcftools merge g1_chromX.vcf.gz g2_chromX.vcf.gz sang_chromX.vcf.gz
The header prints fine, but in the first line I get: FIXME: error parsing DP4 at X:3050056 .. -2

Finally I can successfully bcftools view all 3 files, and bcftools merging just g1.vcf.gz and g2.vcf.gz works just fine.

I was wondering if anyone might have any experience or suggestions that might help me understand the error messages or to merge my 3 vcf files.


Thanks a whole lot in advance!

[TiborNagy]

I think there is some problem with sang.vcf.gz file. Can you check the content of the file? (The reference names are the same?)

[whataBamBam]

Hang on.. my bcftools doesn't have a merge command

And I was actually just looking for a way to merge bcfs..

Samtools / Vcftools sourceforge page doesn't say anything about merge in (I assume( the latest version.. what version are you using here? Where can I get merge??