Question: Warning while finding bcftools consensus
0
gravatar for banerjeeshayantan
2.2 years ago by
banerjeeshayantan170 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 • 535 views
ADD COMMENTlink written 2.2 years ago by banerjeeshayantan170

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 2.2 years ago by Kevin Blighe63k

The vcfs were downloaded from COSMICdb

ADD REPLYlink written 2.2 years ago by banerjeeshayantan170

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 months ago • written 10 months ago by g.barreau0
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