Hi, I've aligned some data using BWA, and am now trying to convert from sam to bam and am getting an error. Any ideas how to rectify this? See below for information.
Thanks!
samtools view -bS file.sam > file.bam
[samopen] SAM header is present: 93 sequences. Parse error at line 95: missing colon in auxiliary data Aborted
head -96 file.sam | tail -5
@SQ SN:chrUn_gl000226 LN:15008 @SQ SN:chr18_gl000207_random LN:4262 @RG ID: LB: SM: PL:ILLUMINA D3B4KKQ1:406:H0YE0ADXX:2:1101:1198:2135 89 chr8 124262197 37 101M = 124262197 0 GACATACAGTATTAAACTGGACTGAATATGAGGANAANCTCTAGTGGTCATTAAACCCCCTCAGAAAGTCTAAGATTCAGAATGTCTCCATCATATTAGAA CEEEEEDCADCCDECCCCCCDCDCDC>A>==5,,#5,#>@E?DGGIIGIHIGIIHIIIIHFIIIIIHIGIGIIIHHIIIIIHFCCGIIHGHHDEBDFD@@@ RG:Z: XT:A:U NM:i:2 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:34C2G63 D3B4KKQ1:406:H0YE0ADXX:2:1101:1198:2135 181 chr8 124262197 0 * = 124262197 0 NTGCCTTNANNNTTNGAGATGTGATTAAGCTTANAACTTTGACCAAAAATTTTACAGTAAAAATTGTTAGAAATGGGTAAAAAAAAAAAAAAAAAAAAAAC ######################################@3(256CDDC@3C@9+38(/DDCC833(>8(3DC?3CA>/BDDDDFHJJJHHHHHFFFFFC@@ RG:Z:
I see you've cross-posted this to the bio-bwa-help mailing list. It'd probably be best to choose one or the other...