bwa alignement outside of the reference sequence

cklopp · 09-14-2011, 06:56 AM

Hi,

Using bwa (Version: 0.5.9-r16) we encountered cases where the proposed alignment position was outside of the reference sequence.
In the example hereunder the alternative alignment position of the read starts, on the forward strand, at position 145240300 on a chromosome of length 145240301

@SQ SN:CHR13 LN:145240301
@SQ SN:CHR14 LN:148515138
@SQ SN:CHR1 LN:295534705
@PG ID:bwa PN:bwa VN:0.5.9-r16
[bwa_aln_core] convert to sequence coordinate... 9.64 sec
[bwa_aln_core] refine gapped alignments... 4.18 sec
[bwa_aln_core] print alignments... HWI-ST314_0106:4:1202:17139:18375#0 16 CHR15 132557769 0 101M * 0 0 ACAGAATTCTATATCCAGTGAGAATATCCTTCAGGTATGAAAGTGAAAAGAGATTTTCTCAGATGAAGGAAAACCGAGTGAATTTGTTGCCAGTGGAGCTA JPJJS`QKQQKQKK[[QJRJJRJK`J`KbK[`Q`RJIIPPP^ceSI^I^IOOHIIOOOOacgINOa_aBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB XT:A:R NM:i:4 X0:i:2 X1:i:1 XM:i:4 XO:i:0 XG:i:0 MD:Z:8G26A50C10T3 XA:Z:CHR13,+145240300,101M,4;CHR14,-18932,101M,5;

Any idea of what happens?

Cheers

Christophe

swbarnes2 · 09-14-2011, 09:25 AM

bwa concatenates the reference sequences together, so if your read hangs off the end of its reference, that'll happen. But bwa should give it a 4 in the binary flag, so that's how you know the mapping isn't quite right.

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09-14-2011, 06:56 AM	#1
cklopp Member Location: Toulouse France Join Date: Sep 2009 Posts: 12	bwa alignement outside of the reference sequence Hi, Using bwa (Version: 0.5.9-r16) we encountered cases where the proposed alignment position was outside of the reference sequence. In the example hereunder the alternative alignment position of the read starts, on the forward strand, at position 145240300 on a chromosome of length 145240301 @SQ SN:CHR13 LN:145240301 @SQ SN:CHR14 LN:148515138 @SQ SN:CHR1 LN:295534705 @PG ID:bwa PN:bwa VN:0.5.9-r16 [bwa_aln_core] convert to sequence coordinate... 9.64 sec [bwa_aln_core] refine gapped alignments... 4.18 sec [bwa_aln_core] print alignments... HWI-ST314_0106:4:1202:17139:18375#0 16 CHR15 132557769 0 101M * 0 0 ACAGAATTCTATATCCAGTGAGAATATCCTTCAGGTATGAAAGTGAAAAGAGATTTTCTCAGATGAAGGAAAACCGAGTGAATTTGTTGCCAGTGGAGCTA JPJJS`QKQQKQKK[[QJRJJRJK`J`KbK[`Q`RJIIPPP^ceSI^I^IOOHIIOOOOacgINOa_aBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB XT:A:R NM:i:4 X0:i:2 X1:i:1 XM:i:4 XO:i:0 XG:i:0 MD:Z:8G26A50C10T3 XA:Z:CHR13,+145240300,101M,4;CHR14,-18932,101M,5; Any idea of what happens? Cheers Christophe

09-14-2011, 09:25 AM	#2
swbarnes2 Senior Member Location: San Diego Join Date: May 2008 Posts: 912	bwa concatenates the reference sequences together, so if your read hangs off the end of its reference, that'll happen. But bwa should give it a 4 in the binary flag, so that's how you know the mapping isn't quite right.