Must always sort before indexing. Use 'samtools sort sample.bam > sorted.bam'.
On Mon, 27 Jul 2015, Komal Rathi wrote: > Hi everyone, > > I am using samtools 1.2/htslib 1.2.1. > > The following is my bam file - mapped to mm10: > samtools view -h sample.bam | less > > @HD VN:1.0 SO:unsorted > @PG ID:GSNAP PN:gsnap VN:2014-12-31 CL:gsnap -d mm10_gmap > --batch=5 --nthreads=10 --format=sam reads_bothclipped_unaligned.fa > @SQ SN:chr1 LN:195471971 > @SQ SN:chr2 LN:182113224 > @SQ SN:chr3 LN:160039680 > @SQ SN:chr4 LN:156508116 > @SQ SN:chr5 LN:151834684 > @SQ SN:chr6 LN:149736546 > @SQ SN:chr7 LN:145441459 > @SQ SN:chr8 LN:129401213 > @SQ SN:chr9 LN:124595110 > @SQ SN:chr10 LN:130694993 > @SQ SN:chr11 LN:122082543 > @SQ SN:chr12 LN:120129022 > @SQ SN:chr13 LN:120421639 > @SQ SN:chr14 LN:124902244 > @SQ SN:chr15 LN:104043685 > @SQ SN:chr16 LN:98207768 > @SQ SN:chr17 LN:94987271 > @SQ SN:chr18 LN:90702639 > @SQ SN:chr19 LN:61431566 > @SQ SN:chrX LN:171031299 > @SQ SN:chrY LN:91744698 > @SQ SN:chrM LN:16299 > HWI-D00712:1134:C6NMYANXX:5:1101:11882:3444 4 * 0 0 > * * 0 0 ACACGCAGCAACCCATCGTT * XO:Z:NM > HWI-D00712:1134:C6NMYANXX:5:1101:10181:1990 4 * 0 0 > * * 0 0 GTTGGGGTCGTAGCCTCGT * XO:Z:NM > HWI-D00712:1134:C6NMYANXX:5:1101:5509:2135 4 * 0 0 > * * 0 0 GCCCACCTGTTAGTGTTGT * XO:Z:NM > HWI-D00712:1134:C6NMYANXX:5:1101:4268:5419 4 * 0 0 > * * 0 0 GTCGATCCGGGCTTTCGTT * XO:Z:NM > HWI-D00712:1134:C6NMYANXX:5:1101:10454:4937 4 * 0 0 > * * 0 0 TCTGCGAACCAACACG * XO:Z:NM > HWI-D00712:1134:C6NMYANXX:5:1101:4687:5341 4 * 0 0 > * * 0 0 TACCTCCTAGTCTTGGTTT * XO:Z:NM > HWI-D00712:1134:C6NMYANXX:5:1101:18702:6367 4 * 0 0 > * * 0 0 TTACCTTCACATGATCTGCT * XO:Z:NM > HWI-D00712:1134:C6NMYANXX:5:1101:4506:7580 4 * 0 0 > * * 0 0 CAGTCACAATTACCGGT * XO:Z:NM > HWI-D00712:1134:C6NMYANXX:5:1101:16573:3163 4 * 0 0 > * * 0 0 CTTTATCAATAGAGAGT * XO:Z:NM > HWI-D00712:1134:C6NMYANXX:5:1101:15871:7576 4 * 0 0 > * * 0 0 ACTTCATGCTCATTGGTTT * XO:Z:NM > HWI-D00712:1134:C6NMYANXX:5:1101:16993:8112 4 * 0 0 > * * 0 0 AGGGATGAGCTCACCGT * XO:Z:NM > HWI-D00712:1134:C6NMYANXX:5:1101:17679:3919 4 * 0 0 > * * 0 0 TAGATCGCTTTGATCCGT * XO:Z:NM > HWI-D00712:1134:C6NMYANXX:5:1101:20428:8085 4 * 0 0 > * * 0 0 CGAGAGAGATTACCTCCGTT * XO:Z:NM > HWI-D00712:1134:C6NMYANXX:5:1101:13289:6144 4 * 0 0 > * * 0 0 ACACCGCTCTAAGAGCGT * XO:Z:NM > > I am trying to index it using: > samtools index sample.bam > > but it is throwing an error: > [E::hts_idx_push] NO_COOR reads not in a single block at the end 1 -1 > > Any help would be much appreciated! > > --Komal > > > ------------------------------------------------------------------------------ > _______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help > ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
