bcftools merge varscan error

[bioinfo-dirty-jobs]

I use bcftools 1.6 (but also on 1.8) for concat two varscan results. I have this error. No variant are present on the ouptut after merging. Here you have the error

E::get_intv] Failed to parse TBX_GENERIC, was wrong -p [type] used?
The offending line was: "chr12  11903737    .   T   G   .   PASS    DP=61;SOMATIC;SS=2;SSC=7;GPV=1E0;SPV=1.9048E-1  GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:28:20:0:0%:16,4,0,0   0/1:.:33:14:2:12.5%:13,1,2,0"
[E::get_intv] Failed to parse TBX_GENERIC, was wrong -p [type] used?
The offending line was: "chr12  21639528    .   G   GA  .   PASS    DP=50;SOMATIC;SS=2;SSC=7;GPV=1E0;SPV=1.8039E-1  GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:20:20:0:0%:4,16,0,0   0/1:.:30:24:3:11.11%:10,14,1,2"
[

[pd3]

Most likely the file is not correctly indexed. You can try tabix file.vcf.gz chr12:11903737-11903737 to verify, or just reindex again bcftools view broken.vcf.gz -Oz -o fixed.vcf.gz && bcftools index fixed.vcf.gz

[bioinfo-dirty-jobs]

@pd3 I try the example but I'm not able to resolve... I create a small example of the files

bgzip  fixa.vcf 
bgzip  fixb.vcf 
 tabix fixa.vcf.gz 
 tabix  fixb.vcf.gz 
bcftools concat -a fixa.vcf.gz fixb.vcf.gz > mitico.vcf
[E::get_intv] Failed to parse TBX_GENERIC, was wrong -p [type] used?
The offending line was: "chr1   2489919 .   G   A   .   PASS    DP=33;SOMATIC;SS=2;SSC=7;GPV=1;SPV=0.17235  GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:19:19:0:0%:3,16,0,0   0/1:.:14:12:2:14.29%:4,8,1,1"
[E::get_intv] Failed to parse TBX_GENERIC, was wrong -p [type] used?
The offending line was: "chr1   26128484    .   CTT C   .   PASS    DP=62;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.087615    GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:37:25:0:0%:22,3,0,0   0/1:.:25:18:3:14.29%:18,0,3,0"

Here you can found the test files files test

[pd3]

I suggested above the command to use, bcftools index instead of tabix, have you tried that? Also in your example the second file is indexed with gzip, I assume it's just a typo.

Anyway, the indexes of the files you provided are really not functional. Maybe some old version of tabix was used? Try tabix --version. Both bcftools index and tabix work for me.

[bioinfo-dirty-jobs]

@pd3 I use this version of tabix

rogram: tabix (TAB-delimited file InderXer)
Version: 0.2.5 

I use the bioconda version