Edit erroneous line using bcftools

Question

[Claire1203]

When handling a vcf file using bcftools, I get the following error:

[W::vcf_parse_format_fill5] Extreme FORMAT/AD value encountered and set to missing at 2:134461416
[E::vcf_parse_format_check7] Number of columns at 2:134461416 does not match the number of samples (343 vs 1842)
Error: VCF parse error

It seems like the line in vcf file for chr2, pos134461416 is malformed. How do I skip that row and ask bcftools to continue to parse the rest of the file? I tried reading up until pos 134461416, and that work just fine. But I want to be able to read information beyond pos 134461417. Or would it be possible to use other tools like grep or awk to clip out the erroneous line? Thank you so much in advance for the help!

Answer 1

[Mensur Dlakic]

This might work:

sed -e '134461416d' < old_file.vcf > new_file.vcf