DiscoSNP++ 2.1.7 vs 2.2.0 huge difference in the number of SNPs called

Question

[tkitapci]

Hi,

I run discoSNP++ using the provided run_discoSNP++.sh script with all default parameters on the same dataset twice using versions 2.1.7 and 2.2.0.

In the VCF file created by 2.1.7 I got 865,316 SNPs while 2.2.0 calls 72,151 SNPs. Is this expected? Is 2.2.0 has much strict parameters for calling SNPs?

Thanks

Best Regards
T. Hamdi Kitapci

Answer 1

[pierre.peterlongo]

Hi,

One of the major novelty in disco 2.2.0 is that it automatically detects the threshold coverage under which k-mers are removed as they are considered as containing a sequencing error.

In 2.1.7 this value is 3 by default. In 2.2.0, this value can be found in the log (line starting by "thresholds").

Regarding your results, two possibility (co-)exist:

• variants predicted only by 2.1.7 are in fact generated by sequencing errors, they are false positives and it's a good thing they were non predicted in 2.2.0
• the automatic threshold detection was too stringent and, by consequence, real k-mers were removed and associated variants were not found.

This is difficult to conclude without a deeper look into your study details, the automatic c value, and the data complexity and coverage.

Pierre

[tkitapci]

Hi Pierre,

Thanks a lot for the clarification I will keep this in mind for my analysis.

Thanks

Best Regards

T. Hamdi Kitapci