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Old 06-18-2017, 11:47 PM   #1
Junior Member
Location: turkey

Join Date: May 2017
Posts: 1
Unhappy Low number of variants taken from high GB data- NextSeq 500


I got 112GB raw data from nextera rapid capture enrichment of nextseq500. FastQ files are approximately 7-9 GB. When I try to annotate variants, the number of variants are nearly 200.000, which is quite low for an exome sequencing result. It is like a bioinformatic error that cannot interpret the variants from the data. Or could it be caused by something else?

Two samples- both have 8GB FASTQ- one has 200.000 variants, other has 1.000.000 variants. How could it be possible ?


Last edited by GizemGoles; 06-19-2017 at 11:31 PM.
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Old 06-21-2017, 03:48 AM   #2
Senior Member
Location: Germany

Join Date: Oct 2008
Posts: 415

From exomes I have seen on that platform about 50000 good variants are to be expected. 1m is way too high for an exome.

Perhaps you need to filter more on quality, I would recommend filtering with vt etc. Also check the calls in a genome browser.

colindaven is offline   Reply With Quote

illumina, low data, nextseq500

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