Hi，i use the snpsift to annotate the vcf file ,it's very useful ;but i found that the same INFO/TAG in both anno.vcf and input.vcf，such as:
a.vcf INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
b.vcf INFO=<ID=AF,Number=A,Type=Float,Description="Alternate allele frequency in samples">
i use the annotate a.vcf by use the INFO/AF in the b.vcf ,so the INFO/AF in a.vcf is overwriten by the snpsift.
i try to use the bcftools annotate to rename the INFO/AF in a.vcf, but the Contig is not in a.vcf, bcftools annotate get the error:
Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
Add the header is more troublesome. Is there other way to rename the INFO/AF in a.vcf?
Thanks!
Hi，i use the snpsift to annotate the vcf file ,it's very useful ;but i found that the same INFO/TAG in both anno.vcf and input.vcf，such as:
a.vcf INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
b.vcf INFO=<ID=AF,Number=A,Type=Float,Description="Alternate allele frequency in samples">
i use the annotate a.vcf by use the INFO/AF in the b.vcf ,so the INFO/AF in a.vcf is overwriten by the snpsift.
i try to use the bcftools annotate to rename the INFO/AF in a.vcf, but the Contig is not in a.vcf, bcftools annotate get the error:
Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
Add the header is more troublesome. Is there other way to rename the INFO/AF in a.vcf?
Thanks!