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I'm processing 3 BAM files mapped with bwa 0.7.17-r1198-dirty , markduplicate with picard 2.19.0 , and realigned around indels with GATK3.8.
bcftools Version: 1.9-124-g3231c34 (using htslib 1.9-133-g9af328a-dirty)
I'm calling bcttools mpileup:
bcftools mpileup --bam-list "bam.list" --adjust-MQ 50 --redo-BAQ \
--fasta-ref "/scratch/BIRD/lindenbaum-p/REFERENCES/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta" --min-MQ 30 \
--regions "chr10:47870368-124121200" -O u -a INFO/AD -a FORMAT/AD -a FORMAT/DP -a FORMAT/SP > out.bcf
I got an error:
I modified htslib/sam.c line 3046 to get the name of the bam:
if(!(a->end-1 == a->s.end)) {
fprintf(stderr,"[FAIL]%s:%d\n",__FILE__,__LINE__);
fprintf(stderr,"%s\n",bam_get_qname(&(a->b)));
exit(-1);
}
the sam record is:
X2:1:HM3K3CCXY:7:2207:7710:28277 163 chr10 56543198 60 49M1D26M6I14M3D56M = 56543348 301 ATGTGTACACATATAATATATACATATGTATGTACACATATAATATATAATATATACATATGTATATATCATTATATATACATATATATGTATATATTATATATACATATGTATATATGTATATAATATATGTAAATAATATATACATATA AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJFJJFJJAAAFFJF--7<FAF-<7AAFAJ77<F< MC:Z:151M MD:Z:49^C20A19^ATA56 PG:Z:MarkDuplicates RG:Z:C0009H8 NM:i:11 MQ:i:60 AS:i:112 XS:i:0
X2:1:HM3K3CCXY:7:2207:7710:28277 83 chr10 56543348 60 151M = 56543198 -301 AATATTGTATACAATATGTATTATTCAAATAATACATAATATTACATAATATGTATATTTATATTTATATTACATATTATATTATATTATATTACATATTACATTTATATTACATATTACAAATAATACATAATATTGTATACACATATAA AJJJJJJAAJJFFJJ<JFJJJJJFFJFFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA MC:Z:49M1D26M6I14M3D56M MD:Z:151 PG:Z:MarkDuplicatesRG:Z:C0009H8 NM:i:0 MQ:i:60 AS:i:151 XS:i:29
if I create a minimal bam with this record, there is no error
if I mpileup in the region again around the bam record (a few KB) , there is no error (?)
How can I find the cause of the problem ?
Thanks.
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