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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