Hello,
I got an error when indexing my sorted BAM file.
> samtools index file.bam
[E::hts_idx_push] NO_COOR reads not in a single block at the end 0 -1
I tried to check the validity of the file with picard-tools:
> java -jar ValidateSamFile.jar I=file.bam IGNORE_WARNINGS=true
ERROR: Record 90709, Read name seq40369#11#7696, The record is out of
[coordinate] order, prior read name [seq28047#7#2353], prior coodinates
[-1:0]
The start coordinate of this read is higher than 1 billion:
seq40369#11#7696 272 chrUn *1024548131* 1 27M * 0 0
GTTGTCTCTGATTCAGAATCATACTTA IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0
XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:27 YT:Z:UU
I retrieved identical problems with bedtools...
Do you have already encountered this bug ?
Thanks,
Olivier
--
========================================================
Olivier RUÉ
INRA - MIAT - Plateforme Bioinfo-Genotoul
Chemin de Borde-Rouge - Auzeville - CS 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel: +33 (0)5.61.28.55.49
http://www.bioinfo.genotoul.fr/
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