BWASW more reads in the output SAM file than in the input file

nanto · 09-17-2012, 06:24 AM

When running BWA I get normal total number of reads (the same as in the input file).

But when running BWASW alignment I get this:

(that's from samtools flagstat)

56125 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
30118 + 0 mapped (53.66%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

My input number of reads loaded to BWA was 45997. How come I got over 80k?

gaffa · 09-17-2012, 08:06 AM

BWA-SW performs local alignment and can output several alignments per input read/sequence. So a given read or different parts of a read can be aligned to different places, which are all included in the output file.

nanto · 09-18-2012, 01:41 AM

I also heard that with extremely long reads bwa-sw can give not very reliable output. Is there any sense in browsing reads up to a given length, or it will change nothing, at will only consume my time.

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09-17-2012, 06:24 AM	#1
nanto Member Location: Wageningen, Netherlands Join Date: Sep 2012 Posts: 19	BWASW more reads in the output SAM file than in the input file When running BWA I get normal total number of reads (the same as in the input file). But when running BWASW alignment I get this: (that's from samtools flagstat) 56125 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 30118 + 0 mapped (53.66%:-nan%) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (-nan%:-nan%) 0 + 0 with itself and mate mapped 0 + 0 singletons (-nan%:-nan%) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) My input number of reads loaded to BWA was 45997. How come I got over 80k?

09-17-2012, 08:06 AM	#2
gaffa Member Location: Gothenburg/Uppsala, Sweden Join Date: Oct 2010 Posts: 82	BWA-SW performs local alignment and can output several alignments per input read/sequence. So a given read or different parts of a read can be aligned to different places, which are all included in the output file.

09-18-2012, 01:41 AM	#3
nanto Member Location: Wageningen, Netherlands Join Date: Sep 2012 Posts: 19	I also heard that with extremely long reads bwa-sw can give not very reliable output. Is there any sense in browsing reads up to a given length, or it will change nothing, at will only consume my time.