bcftools usage examples - lacking steps?

[henrikstranneheim]

I could only get it to wrk using these commands:

$bcftools query -f'%CHROM\t%POS\t%REF,%ALT\t%INFO/AF\n' ../develop/references/anon-SweGen_STR_NSPHS_1000samples_snp_freq_hg19.vcf.gz | bgzip -c > ../develop/references/anon_SweGen_161019_snp_freq_hg19.tab.gz

$tabix -s 1 -b 2 -e 2 ../develop/references/anon_SweGen_161019_snp_freq_hg19.tab.gz

$bgzip -c ../develop/118/analysis/118/bwa/118_sorted_md_brecal_gvcf_vrecal_comb_BOTH.vcf > test.vcf.gz

$tabix -p vcf test.vcf.gz

$bcftools roh --AF-file ../develop/references/anon_SweGen_161019_snp_freq_hg19.tab.gz -I test.vcf.gz -s 118-1-2A > 118_sorted_md_brecal_gvcf_vrecal_comb_BOTH.roh

Which is different from your example. Still valid or should I have done something differently?

[dnil]

Looks about right. The reason appears is a version difference in bcftools.
Worked fine without indexing in bcftools 1.2, but seems to have issues in 1.3! Nice catch!

[dnil]

Oh, and if you are using a compressed bcf, no need to index..