how to deal with secondary alignment when calling snps

Question

[Kritika]

I have many type secondary alignment like this how to deal with such type of alignment when i am doing SNP calling

E00477:196:HCYTLCCXY:1:1101:29488:52959 83  D06 **61344168  60  150M    =   61343983    -335** GAAAGACTAAATTCCAAATATAAAAAGCATATAAAAATTTGAAATAAAATATATTTTAAACTTTAATTTTTTATTTTATAAATTAATATAAATAAATAATTAACCAAGTCAATTTAGATATAATTTAATTGTGCTGATTATTCTCGCAGAFFJF-JFFJF<7<FJJJFFJJJJJF7-JJJJJJJJJ<FJJJJJJJFFJJJJJ<J-<<JJJA-JJJF-JJFAJJJJJJJJJJJJJFJFFJJJJJJJJJF-7FFFFJAJ<-FJA-FJFJJJJJJJJJJJJJJAFFJFJJJJJJJ<JJAFA-A NM:i:1MD:Z:108G41 MC:Z:150M AS:i:145    XS:i:89

E00477:196:HCYTLCCXY:1:1101:29488:52959 163 D06 **61343983  60  150M    =   61344168    335**   TCAAAATAATGCCATCATTTTTTTCTTACGAACACGAGTCCAACAAAAAAAAATTTATCATAATGAATTTGAATGGATGTTTTTAAGATAAATTCTAATCAGTATTTATAAAAGAAATTTAATGGTGGAAACAATTGAACCTGAAATTTT  A-A<AFJJ-AAFJA<AJJJJJJFJFJJFJFJJA<A-FAJAFAJJJJ<JJJFJFFFFJF-F<FFFA-77AFFFJJJF7AFJAAJJ-A7A-7FFF-7FJJ--7-AF<7F<JFJJJJFAA-7FAF-77<-7FJF-F--FAFF-----<A-A<-  NM:i:4MD:Z:8C44A34A53C7 MC:Z:150M   AS:i:130    XS:i:21

[Pierre Lindenbaum]

what do you mean with "secondary alignment" ? those reads are flagged with 83 and 163: these are primary alignments.

[Kritika]

61344168 60 150M = 61343983 -335

61343983 60 150M = 61344168 335

Actaully i was talking about this i am dealing with homoelogous genome data

[Pierre Lindenbaum]

I still don't get your problem. These are the coordinates of two paired-end reads for the same segment.

[WouterDeCoster]

In the case of secondary alignments your variant caller should take care of those.