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!
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!
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