Missing INS in IGV?

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5.5 years ago

timothy.tl.ng ▴ 10

Hi all,

I am new to this community. Nice to meet you all.

I am working on detection of SNP and INDEL of samples by aligning the read sequences (generated from nanopore sequencing) to the reference bacteria genome. After the alignment with BWA and the aligned read sorting with igvtools, I can see the alignment on IGV windows.

When I move the cursor to a position on the coverage track, I see the count of A, T, C, G, INS, and DEL. Interestingly, for example, I see 44 INS is reported on the position and I manually count the INS. I can get around 30 INS with my sight. Do I miss anything on the setting? The same happened in other mutation type (SNP and DEL). Your help will be highly appreciated.

Timothy Ng

sequencing alignment genome • 1.2k views

ADD COMMENT • link 5.5 years ago by timothy.tl.ng ▴ 10

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It's likely that IGV is hiding some of the alignments due to them being secondary alignments or being tagged as having quality issues. Go into the preferences in IGV and check to ensure that all alignments will be shown.

ADD REPLY • link 5.5 years ago by Devon Ryan 104k

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Hi Devon,

Thank you for your infomation, I think I got it.

Timothy Ng

ADD REPLY • link 5.5 years ago by timothy.tl.ng ▴ 10

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