Hi Kerry, what does `head regions.txt` look like? Any chance you could send a small test case for debugging?
Petr On Thu, 2015-07-02 at 09:52 -0700, Kerry Deutsch wrote: > 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 > ------------------------------------------------------------------------------ > Don't Limit Your Business. Reach for the Cloud. > GigeNET's Cloud Solutions provide you with the tools and support that > you need to offload your IT needs and focus on growing your business. > Configured For All Businesses. Start Your Cloud Today. > https://www.gigenetcloud.com/ > _______________________________________________ Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
