< and > in the value of the added header entries by the CrossMap causes Bcftools to produce error and ignore those header lines. Deleting these characters resolves the issue.
$ CrossMap.py -v
CrossMap 0.6.1
$ bcftools -v
bcftools 1.14
Using htslib 1.14
Copyright (C) 2021 Genome Research Ltd.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Errors while outputting the header (see E::bcf_hdr_parse_lines):
$ bcftools view -h decode_variants_autosomes.EVA.fixed.B38.crossmap.vcf | tail
[E::bcf_hdr_parse_line] Could not parse the header line: "##liftOverProgram=<CrossMap,version=0.6.1,website=https://sourceforge.net/projects/crossmap>"
[E::bcf_hdr_parse_line] Could not parse the header line: "##liftOverChainFile=</Users/gungor/References/hg18ToHg38.over.chain.gz>"
[E::bcf_hdr_parse_line] Could not parse the header line: "##originalFile=<decode_variants_autosomes.EVA.fixed.vcf.gz>"
[E::bcf_hdr_parse_line] Could not parse the header line: "##targetRefGenome=</Users/gungor/References/B38.p13.fa>"
[E::bcf_hdr_parse_line] Could not parse the header line: "##liftOverDate=<December08,2021>"
##contig=<ID=chrU_KI270755.1,length=36723,assembly=B38.p13.fa>
##contig=<ID=chrU_KI270756.1,length=79590,assembly=B38.p13.fa>
##contig=<ID=chrU_KI270757.1,length=71251,assembly=B38.p13.fa>
##contig=<ID=chrX,length=156040895,assembly=B38.p13.fa>
##contig=<ID=chrY,length=57227415,assembly=B38.p13.fa>
##contig=<ID=chrY_KI270740.1_random,length=37240,assembly=B38.p13.fa>
##contig=<ID=chrhs38d1,length=6030922,assembly=B38.p13.fa>
##bcftools_viewVersion=1.14+htslib-1.14
##bcftools_viewCommand=view -h decode_variants_autosomes.EVA.fixed.B38.crossmap.vcf; Date=Wed Dec 8 16:44:49 2021
#CHROM POS ID REF ALT QUAL FILTER INFO
After replacing the header with the entries without those characters:
header.txt
$ tail header.txt
##contig=<ID=chrX,length=156040895,assembly=B38.p13.fa>
##contig=<ID=chrY,length=57227415,assembly=B38.p13.fa>
##contig=<ID=chrY_KI270740.1_random,length=37240,assembly=B38.p13.fa>
##contig=<ID=chrhs38d1,length=6030922,assembly=B38.p13.fa>
##liftOverProgram=CrossMap,version=0.6.1,website=https://sourceforge.net/projects/crossmap
##liftOverChainFile=/Users/gungor/References/hg18ToHg38.over.chain.gz
##originalFile=decode_variants_autosomes.EVA.fixed.vcf.gz
##targetRefGenome=/Users/gungor/References/B38.p13.fa
##liftOverDate=December08,2021
#CHROM POS ID REF ALT QUAL FILTER INFO
Bcftools outputting the header (no E::bcf_hdr_parse_line):
$ bcftools reheader -h header.txt decode_variants_autosomes.EVA.fixed.B38.crossmap.vcf | bcftools view -h | tail
##contig=<ID=chrY_KI270740.1_random,length=37240,assembly=B38.p13.fa>
##contig=<ID=chrhs38d1,length=6030922,assembly=B38.p13.fa>
##liftOverProgram=CrossMap,version=0.6.1,website=https://sourceforge.net/projects/crossmap
##liftOverChainFile=/Users/gungor/References/hg18ToHg38.over.chain.gz
##originalFile=decode_variants_autosomes.EVA.fixed.vcf.gz
##targetRefGenome=/Users/gungor/References/B38.p13.fa
##liftOverDate=December08,2021
##bcftools_viewVersion=1.14+htslib-1.14
##bcftools_viewCommand=view -h; Date=Wed Dec 8 16:45:30 2021
#CHROM POS ID REF ALT QUAL FILTER INFO
liguowang
commented
2 years ago
<and>in the value of the added header entries by the CrossMap causes Bcftools to produce error and ignore those header lines. Deleting these characters resolves the issue.Errors while outputting the header (see
E::bcf_hdr_parse_lines):After replacing the header with the entries without those characters:
header.txt
Bcftools outputting the header (no
E::bcf_hdr_parse_line):