[Samtools-help] bcftools annotate segfaults with tab-delimited file

[Roderick Y. <rod...@si...>]

Dear Samtools Team,

I am attempting to annotate a small vcf file with a bgzipped, tabix-indexed tab-delimited file.  However, bcftools  annotate (version 1.3.1) immediately prints "Segmentation fault" and exits without any other error messages.  I suspect this may be due to the presence of characters in the tab-delimited file's annotations that may not follow the VCF 4.2 spec about what is permitted in an INFO field value, but I am not sure.  Does bcftools annotate properly handle annotations in a tab-delimited file that contain unusual characters, or do I have to convert the annotations myself?  In addition, if bcftools annotate does not handle unusual characters, would this cause a segfault as described?

The command I ran was:
[ryao@qlogin5 TOF_reannotation_test]$ bcftools annotate -O v -a ./MitImpact_db_2.5_sorted_converted.txt.gz -c "$mitimpact_fields" -h ./mitimpact_bcftools_header.txt ./annotation_test_sites.vcf > annotation_test_sites_reann.vcf
Segmentation fault

$mitimpact_fields was previously defined but is very long.

The first few lines of the input VCF file look like:
##fileformat=VCFv4.2
##contig=<ID=chrM,length=16571>
##contig=<ID=chr1,length=249250621>
##contig=<ID=chr2,length=243199373>
##contig=<ID=chr3,length=198022430>
##contig=<ID=chr4,length=191154276>
##contig=<ID=chr5,length=180915260>
##contig=<ID=chr6,length=171115067>
##contig=<ID=chr7,length=159138663>
##contig=<ID=chr8,length=146364022>
##contig=<ID=chr9,length=141213431>
##contig=<ID=chr10,length=135534747>
##contig=<ID=chr11,length=135006516>
##contig=<ID=chr12,length=133851895>
##contig=<ID=chr13,length=115169878>
##contig=<ID=chr14,length=107349540>
##contig=<ID=chr15,length=102531392>
##contig=<ID=chr16,length=90354753>
##contig=<ID=chr17,length=81195210>
##contig=<ID=chr18,length=78077248>
##contig=<ID=chr19,length=59128983>
##contig=<ID=chr20,length=63025520>
##contig=<ID=chr21,length=48129895>
##contig=<ID=chr22,length=51304566>
##contig=<ID=chrX,length=155270560>
##contig=<ID=chrY,length=59373566>
#CHROM             POS        ID            REF         ALT         QUAL    FILTER   INFO
chrM     3607       .               G             A             .               .               .
chr1       10583    .               G             A             .               .               .
chr1       12783    .               G             A             .               .               .
chr1       13116    .               T              G             .               .               .
chr1       13118    .               A             G             .               .               .
chr1       13302    .               C             T              .               .               .
chr1       13656    .               CAG       C             .               .               .
chr1       13896    .               C             A             .               .               .
chr1       13957    .               TC           T              .               .               .
chr1       14397    .               CTGT     C             .               .               .
chr1       14907    .               A             G             .               .               .
chr1       15211    .               T              G             .               .               .
chr1       15274    .               A             G,T         .               .               .

The header file and database file are relatively long, so I won't include them to avoid readability issues.  If you need to take a look at them, I can attach them to a follow-up e-mail upon request.

Regards,
Roderick Yao

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