SNPEff not showing SNP
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6.2 years ago

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

snpEff variant-annotation SNP • 1.7k views
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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

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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.

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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?

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