Question: SNPEff not showing SNP
gravatar for sanjay.bpkihs
23 months ago by
sanjay.bpkihs0 wrote:

Hi I ran a command:

java -Xmx4g -jar snpEff.jar Mycobacterium_tuberculosis_h37rv_gca_000277735 variants.vcf > R_variants.ann.vcf -v

to annotate variants in vcf file that was produced using command:

java -jar VarScan.v2.3.9.jar mpileup2cns mydata.mpileup --min-coverage 5 --min-var-freq 0.90 --p-value 0.005 --variants > variants.vcf

The snpEff output shows SNP=0 INS=1508 Del=51 MIXED=6. However in varscan, for the same file there were 1484 SNP and 75 Indels out of 1550 SNV.

i wonder if anyone can help me get through it.

Thank you

ADD COMMENTlink modified 21 months ago by cpad011212k • written 23 months ago by sanjay.bpkihs0

Hello sanjay,

please edit your post in a way that it is more readable. Be aware of the button for formating code.

Could you please post some example lines of your vcf you want to annotate and the annotatet ones?

fin swimmer

ADD REPLYlink written 23 months ago by finswimmer13k

How to Use Biostars, Part-I: Questions, Answers, Comments and Replies

SNPEff just annotate the data. So defining if it is SNP or not is based on the variant caller, and SNPEff will annotate the result of the incident.

ADD REPLYlink modified 23 months ago • written 23 months ago by Medhat8.6k

Please post an example VCF record classified "ins" by snpEff and "SNP" (SNV) by varscan. In general, SNV annotation is pretty straight forward. I am not sure there would be that much discrepancy between snpEff and Varscan output for SNVs (0 vs 1484). Is VCF left aligned?

ADD REPLYlink modified 21 months ago • written 21 months ago by cpad011212k
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