How to create an indexed VCF for BaseRecalibrator?
First, I searched the forum for answers to my question, but none of them seem to be working. I have a non-model organism and I'm trying to use
BaseRecalibrator as recommended in the manual: run the
HaplotypeCaller, filter the most robust variants and apply
BaseRecalibrator using these variants as a database.
Let's say I select the most robust variants based on QUAL>10000 (an arbitrary limit). I use bcftools to do this:
bcftools filter --include 'QUAL>10000' --output-type v --output qual.vcf combined.vcf
This creates a new uncompressed VCF file with filtered variants. When I try it with
BaseRecalibrator -nt 1 -nct 8 -R genome/A.pisum_genome_AphidBase_fixed.fasta -I bam/F1avr.bam -knownSites vcf/qual.vcf -o bam/F1avr.recal.table
I get an error
ERROR MESSAGE: An index is required, but none found., for input source: .../vcf/qual.vcf
I tried creating an index with
BaseRecalibrator does not recognise a
csi index. Renaming
.idx threw an error about an incompatible index.
I tried following one of the suggestions from the forum and used a
.bgzip compressed VCF. Again, "no index" error. When I created a
bcf file with
bcftools, it was not recognised.
I'm running out of options. What do I do?