Is BWA consider insert size when define read mapped in proper pair

When BWA assign flag 2 for read mapped in proper pair Does it take in consideration the insert size? (from searching I think yes), But in the read below I see that the insert size is 6.
So what define proper insert size? Is't small value of insert size could point to a potential deletion? (like the case below)

HISEQ1:19:H8VDAADXX:2:2106:8906:10302 99 1 7559182 30 57M4I75M4D12M = 7559060 6 GGTGTGATCCTGGTGTGCGTGTGTACGTATATGAGTGTGTGTGTGCATGTGTGTCCATGAGTGAGTGTGCAGAGAGGATGGTGTGATCCTGGTGTGCATGTGTATGTATTTGAGTGTGTGTGTGCATGTGTGTACATGAGTGTGTAGA @BBFDDFFHHHHHJIIJJJIJIIIJJJIJJJJJIJGGHHGHHIHIJIJJIIIJJJJJJJIIBFCHFHEHBHIHHHHFDFBC>ACDDDCCCCD;<?BCCCA>@5;@C:>>@CD4<:@@A<A<?AA>ADCDDDBDCDDCC:@CCCC2>>3 NM:i:9 MD:Z:105A26^TGAG12 MC:Z:26S18M6D104M AS:i:123 XS:i:108 XA:Z:1,+7559103,148M,9; RG:Z:sample_3

bwa alignment sequencing

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updated 7.8 years ago by Pierre Lindenbaum

• written 7.8 years ago by Medhat

1 answer

if I'm not wrong for each batch of fastq data, bwa use a percentile of the read-length distribution. see:

https://github.com/lh3/bwa/blob/master/bwamem_pair.c#L84

https://github.com/lh3/bwa/blob/master/bwamem_pair.c#L93

https://github.com/lh3/bwa/blob/master/bwamem_pair.c#L99

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written 7.8 years ago by Pierre Lindenbaum

So, The answer is Yes it takes insert size in consideration and it depend on the batch that the read belongs to (in such case 6 will be proper insert size even though it does not fit to overall average of insert sizes in file).

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written 7.8 years ago by Medhat