bcftools consensus still returns “Could not parse the header” error
I attempted to create a consensus fasta file using bcftools, i.e.
bgzip -c All_SRR_SNP_Clean.vcf > All_SRR_SNP_Clean.vcf.gz tabix All_SRR_SNP_Clean.vcf.gz cat $ref| bcftools consensus $vcf_dir/All_SRR_SNP_Clean.vcf.gz > consensus.fasta
where $ref is the path to a Drosophila reference genome fa and the vcf was generated from an mpileup combining 4 different poolseq samples.
I get a parse error message:
[W::bcf_hdr_register_hrec] The type "FLoat" is not supported, assuming "String" [W::bcf_hdr_parse] Could not parse header line: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR5647735.1.realign.bam SRR8439151.1.realign.bam SRR8439156.1.realign.bam [E::bcf_hdr_parse] Could not parse the header, sample line not found Failed to read from /home/mshpak/Lundflies/bams/unsorted/round1 /VCF/Three_Files/All_SRR_SNP_Clean.vcf.gz: could not parse header
Several threads from 2-3 years ago referenced similar errors using bcftools, e.g.
but they don’t indicate a satisfactory resolution. As I have the most recent version of bcftools, it doesn’t seem like the problem has been corrected, so is there a patch or work-around available?
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