I'm trying to use vcf-merge to combine 2 exome capture vcf files (~250K and ~330K in size) before trying it on all 96 samples. I'd appreciate any advice on the best way to do that! I've detailed what I've tried below. My issue seems to be with using tabix to convert the files to .tbi format.
Step 1: BGZIP
So far, I've zipped the files without issue:
bgzip sample1.vcf bgzip sample2.vcf
Step 2: TABIX
When I try to use this command:
tabix -h -p vcf sample1.vcf.gz
the stderr is:
Region 536999277..536999278 cannot be stored in a tbi index. Try using a csi index with min_shift = 14, n_lvls >= 6. tbx_index_build failed: sample1.vcf.gz
Using the -C option which works:
tabix -C -h -p vcf sample1.vcf.gz tabix -C -h -p vcf sample2.vcf.gz
which produces: sample1.vcf.gz.csi sample2.vcf.gz.csi
Step 3: VCF-MERGE
When I use this command:
vcf-merge sample1.vcf.gz.csi sample2.vcf.gz.csi > out.vcf.gz
the merge fails, and I get this stderr:
Broken VCF header, no column names? at /usr/share/perl5/Vcf.pm line 172, <ANONIO> line 1. Vcf::throw(Vcf4_2=HASH(0x5645a760bc38), "Broken VCF header, no column names?") called at /usr/share/perl5/Vcf.pm line 867 VcfReader::_read_column_names(Vcf4_2=HASH(0x5645a760bc38)) called at /usr/share/perl5/Vcf.pm line 602 VcfReader::parse_header(Vcf4_2=HASH(0x5645a760bc38)) called at /usr/bin/vcf-merge line 183 main::init_cols(HASH(0x5645a761f438), Vcf4_2=HASH(0x5645a760b248)) called at /usr/bin/vcf-merge line 279 main::merge_vcf_files(HASH(0x5645a761f438)) called at /usr/bin/vcf-merge line 12
If I exclude the tabix files, the merge still fails and the stderr says:
The column names not tab-separated? Could not load .tbi index of sample1.vcf.gz. The command exited with an error. Is the file tabix indexed?
Any suggestions on how I can correctly merge these files?