Hi all, I have been looking in various forums, yet I didn't find any answer to my troubles using samtools index:
Briefly, I'm aligning small fastq file to a reference genome using BWA. I then create a bam file from the sam BWA output, sort the sam file and try to index the bam file, but I always have this error message: [E::hts_idx_push] NO_COOR reads not in a single block at the end 0 -1 Here are the command lines I used: bwa mem -t 8 -k 19 -c 500 -O 0,0 -E 2,2 -v 1 -T 10 "$GENOME_INDEX" "$FILE_REP"/P1_001.fq > P1_001.sam samtools view -Sb P1_001.sam > P1_001.bam samtools sort P1_001.bam P1_001.sorted samtools index -b P1_001.sorted.bam My bam file looks sorted tho: @HD VN:1.3 SO:coordinate @SQ SN:chrUn LN:1110957068 @SQ SN:chrUn_1 LN:46845775 @SQ SN:chrUn_10 LN:34542469 Does anyone have already experienced this issue ? Regards, J.
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