Is it possible to index VCF files and merged the CNVs therein contained using VCF files created from exome sequencing data

Question

[yawolberg]

Hi,

I am using data generated from using the CNV detection tools, CANOES, CLAMMS, and XHMM to call CNVs from exome sequencing data. I have generated VCF files from BED (output of CLAMMS) and CSV (output of CANOES) files. I tried using BCFtools to merge two VCF files into a single file but then I was told that I need to create index files.

[E::idx_find_and_load] Could not retrieve index file for 'DDD_Africa/yoni_exome_cnv/CANOES_CNVs_filtered1.vcf.gz'

I then tried to index the file using bcftools index

Then it says that it failed to create the index files.

[E::hts_idx_push] Chromosome blocks not contiguous index: failed to create index for 'DDD_Africa/yoni_exome_cnv/CANOES_CNVs_filtered1.vcf.gz'

How do I create index files when I only have VCF files containing a number of CNV variants called from exome data. Is it possible to use bcftools index when I don't have complete chromosome blocks.

[GenoMax]

You can sort and index the files using bcftools : https://samtools.github.io/bcftools/bcftools.html#sort