Warning while finding bcftools consensus

Question

[Gene_MMP8]

I am trying to find bcftools consensus using GRCH38. But I am getting the following error. What does this mean and how to get past it? The command used was: consensus -f grch38.fa CosmicCodingMuts.vcf.gz > real_nbd.fa

Warning: Sequence "CM000672.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000673.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000674.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000675.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000676.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000677.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000678.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000679.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000680.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000681.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000663.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000682.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000683.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000684.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000664.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000665.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000666.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000667.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000668.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000669.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000670.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000671.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000685.2" not in CosmicCodingMuts.vcf.gz
Warning: Sequence "CM000686.2" not in CosmicCodingMuts.vcf.gz

[g.barreau]

Difficult to answer without more details but I have a similar issue where the header has the following value in both the fasta and the vcf:

SLmic1.0_ch05:1-1000000

And upon executing bcftools concensus I get:

Warning: Sequence "SLmic1.0_ch05" not in Parents/p1.on.ref.fb.vcf.gz

So it seems that the ":" in the header is a problem.

Answer 1

[Kevin Blighe]

Most likely CM000672.2 is not recorded in your VCF header, and/or it simply does nt exist in your file in the CHROM field. Can you elaborate on how you produced your VCFs?

[Gene_MMP8]

The vcfs were downloaded from COSMICdb

[Kevin Blighe]

Cool. Can you show the VCF header please?

bcftools view -h cosmic.vcf