Question: Warning while finding bcftools consensus
0
gravatar for banerjeeshayantan
16 months ago by
banerjeeshayantan140 wrote:

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

sequencing next-gen assembly • 350 views
ADD COMMENTlink written 16 months ago by banerjeeshayantan140

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?

ADD REPLYlink written 16 months ago by Kevin Blighe50k

The vcfs were downloaded from COSMICdb

ADD REPLYlink written 16 months ago by banerjeeshayantan140

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.

ADD REPLYlink modified 10 days ago • written 10 days ago by g.barreau0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2213 users visited in the last hour