Hi all -
I'm running into an error that I can't figure out with the following
process:
samtools -ABQ0 -p -m 1 -F 0.0005 --ext-prob 10 --open-prob 10 -t
DP,DV,DPR,INFO/DPR,DP4,SP -g -u -f genome.fa file.bam | bcftools call
--output-type u --keep-alts --format-fields GQ,GP --multiallelic-caller - >
variants_all.bcf
bgzip variants_all.vcf
tabix variants_all.vcf.gz
No errors or warnings from the above.
But,
bcftools filter -R regions.txt -o variants_regions.vcf regions_all.vcf.gz
throws this error midway through processing the file:
bcftools: synced_bcf_reader.c:405: _reader_seek: Assertion `reader->itr'
failed.
Aborted (core dumped)
The partial final line of variants_regions.vcf shows this:
chr4 103537627 . G A 29.6056 PASS
DP=606;SGB=-0.379885;RPB=1;MQB=1;MQSB=0.999158;BQB=1;MQ0F=0;DPR=605,1;AC=0;AN=2;DP4=452,153,0,1;MQ=59
while the corresponding line in variants_all.vcf.gz is this:
chr4 103537627 . G A 29.6056 .
DP=606;SGB=-0.379885;RPB=1;MQB=1;MQSB=0.999158;BQB=1;MQ0F=0;DPR=605,1;AC=0;AN=2;DP4=452,153,0,1;MQ=59
GT:PL:DP:DV:SP:DP4:DPR 0/0:0,255,255:606:1:0:452,153,0,1:605,1
I don't see anything jumping out at me with that line.
I'm running version 1.2 of both samtools & bcftools, with bgzip & tabix
coming from htslib-1.2.1.
Anyone have any ideas?
Thanks!
--
Kerry
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