Entering edit mode
10.1 years ago
Pierre Lindenbaum
160k
I've aligned my reads with two versions of bwa:
- bwa-0.6.2 sampe
- bwa-0.7.5a mem
Here is a screenshot of IGV (it's haloplex, that's why I get those vertical clusters of reads)
http://i.imgur.com/mKVbQRY.pngmd5-0da56900a9b0c721b8487f6814da9a99
sampe found a 21bp deletion (circled in blue) while mem didn't it (see below). How can I explain this ? Here is a comparaison of the reads in that region
#READ-Name compare sampe.sam(chrom:pos=flag/cigar) mem.sam(chrom:pos=flag/cigar)
HWI-1KL149:56:D2513ACXX:1:1105:2873:34609/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:1:1105:2873:34609/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:1:1108:9653:29360/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:1:1108:9653:29360/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:1:1216:11311:17867/1 NE chrom:xxxx530=83/12S57M21D31M chrom:xxxx528=83/10S88M2S
HWI-1KL149:56:D2513ACXX:1:1216:11311:17867/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:1:1216:5061:40076/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:1:1216:5061:40076/2 NE chrom:xxxx389=163/95M5S chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:1:1304:1508:5563/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:1:1304:1508:5563/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:1:1316:14376:53279/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:1:1316:14376:53279/2 NE chrom:xxxx389=163/97M3S chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:1:2106:17460:28922/1 EQ chrom:xxxx817=83/100M chrom:xxxx817=83/100M
HWI-1KL149:56:D2513ACXX:1:2106:17460:28922/2 NE chrom:xxxx555=163/32M21D60M8S chrom:xxxx555=163/32M21D68M
HWI-1KL149:56:D2513ACXX:1:2107:1791:84494/1 NE chrom:xxxx522=83/4S65M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:1:2107:1791:84494/2 NE chrom:xxxx389=163/42M58S chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:1:2116:18094:31238/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:1:2116:18094:31238/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:1:2206:2114:60989/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:1:2206:2114:60989/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:1:2211:4062:21441/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:1:2211:4062:21441/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:1:2213:5370:62530/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:1:2213:5370:62530/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:1:2303:12033:82789/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:1:2303:12033:82789/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:1:2304:9324:7003/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:1:2304:9324:7003/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:1:2314:4989:17142/1 NE chrom:xxxx528=83/10S59M21D31M chrom:xxxx528=83/10S88M2S
HWI-1KL149:56:D2513ACXX:1:2314:4989:17142/2 NE chrom:xxxx389=163/82M18S chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:2:1102:4558:67357/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:2:1102:4558:67357/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:2:1107:18152:71354/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:2:1107:18152:71354/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:2:1209:16449:9982/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:2:1209:16449:9982/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:2:1314:17951:51466/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:2:1314:17951:51466/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:2:2102:20151:30908/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:2:2102:20151:30908/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:2:2105:4479:17460/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:2:2105:4479:17460/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:2:2109:13921:24074/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:2:2109:13921:24074/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:2:2112:5665:25455/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:2:2112:5665:25455/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:2:2301:12793:90459/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:2:2301:12793:90459/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
HWI-1KL149:56:D2513ACXX:2:2305:1854:98774/1 NE chrom:xxxx518=83/69M21D31M chrom:xxxx518=83/98M2S
HWI-1KL149:56:D2513ACXX:2:2305:1854:98774/2 EQ chrom:xxxx389=163/100M chrom:xxxx389=163/100M
Furthermore, in 'sampe' some reads have been soft clipped in 3' (red circle), those reads have a poor quality in 3'
@HWI-1KL149:56:D2513ACXX:2:2313:19605:15345 2:N:0:GATGAATC
AAGCCGCGAGGCCGGAATGCGGCGGGGGGAAGTAGACCCGGCGAAAGTAATACAATGCGGATTTTGGAGGGAGAAGCAAGAATAACCTTGATGGCATGCA
+
@@?DB@DDCAF,2A:AEA3AE@A@BEE>B:BGC:@?FFCA';8B7;BB####################################################
does this explain the soft-clipping ?
Pierre