Annotating big VCF file hg38

Question

[mel22]

Hi , Please I need to annotate a vcf file ( phased sequencing data of about 1000 persons ). Its a hg 38 built , I tried with this file common_all_20180418.vcf.gz and this command :

bcftools annotate -a common_all_20180418.vcf.gz -c ID mydata.phased.call.allchr.vcf.gz --output-type z -o mydata_dbSNP151.vcf.gz

and i get this error message

[W::hts_idx_load2] The index file is older than the data file: mydata.phased.call.allchr.vcf.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: mydata.phased.call.allchr.vcf.gz.tbi
[E::bgzf_flush] File write failed (wrong size)
[E::vcf_parse_format] Number of columns at chr14:77174450 does not match the number of samples (60 vs 929)
[E::bgzf_flush] File write failed (wrong size)

Do you have any idea how to solve this ???!!

Thank you

Answer 1

[ATpoint]

Delete index, make a new one, using tabix. The error message is quite clear towards the underlying error.

[mel22]

Thank you ATpoint, I will try this