Question: Why FS is low when reads aligned from strand seem biased?
0
gravatar for Sharon
21 months ago by
Sharon460
Sharon460 wrote:

Hi Everyone

I wonder why the fisher strand is low whcih means no bias given the number of reads aligned from each strand which show bias? The low coverage is because of the GC content, but why FS is low here?

                       Strand+             Strand-                  FS(FisherStrand)
Sample1 
         Ref              1                        5                            3.5
         Alt              3                       12                                                        
Sample2
         Ref              2                        6                            3.5
         Alt              4                        2  
Sample3
         Ref              2                        8                            3.5        
         Alt              1                        6

Thanks

vcf variant calling exome • 410 views
ADD COMMENTlink modified 21 months ago by finswimmer13k • written 21 months ago by Sharon460
1
gravatar for finswimmer
21 months ago by
finswimmer13k
Germany
finswimmer13k wrote:

The fisher strand test does not describe whether you have significant more reverse or forward reads. It checks whether the ratio between reads having the REF and those having the ALT differ significant between the two strands.

fin swimmer

ADD COMMENTlink written 21 months ago by finswimmer13k

Got it, thanks finswimmer.

ADD REPLYlink written 21 months ago by Sharon460
1

Fine :)

Please mark my answer as accepted if you find it helpful.

fin swimmer

ADD REPLYlink written 21 months ago by finswimmer13k
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