Low number of variants taken from high GB data- NextSeq 500

[GizemGoles]

Hi,

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 ?

Thanks

[colindaven]

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.

Best,
Colin