SnpEff does not create htmlStats
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6 weeks ago
Ric ▴ 370

SnpEff does not create htmlStats with the below command:

$ snpEff eff -Xmx20G LAB330 LabUsa16cWild01-20_L-Q.vcf | head
##fileformat=VCFv4.0
##filedate=20210414
##source=SGSautoSNP
##reference=NbLab330.genome.softmasked.fasta
##phasing=allhomozygote
##INFO=<ID=DP,Number=1,Type=Integer,Description="Read depth over all samples">
##INFO=<ID=PL,Number=0,Type=String,Description="Panel">
##SnpEffVersion="5.0e (build 2021-03-09 06:01), by Pablo Cingolani"
##SnpEffCmd="SnpEff  LAB330 LabUsa16cWild01-20_L-Q.vcf "
##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">
...
NbLab330C06 30727797 NbLab3300177406 ? C,T 102.0 . DP=239;ANN=C|intergenic_region|MODIFIER|gene.49723.0-gene.49722.4|gene.49723.0-gene.49722.4|intergenic_region|gene.49723.0-gene.49722.4|||n.30727797?>C||||||,T|intergenic_region|MODIFIER|gene.49723.0-gene.49722.4|gene.49723.0-gene.49722.4|intergenic_region|gene.49723.0-gene.49722.4|||n.30727797?>T|||||| GT:DP 1/1:7 1/1:25 2/2:31 2/2:311/1:46 2/2:27 1/1:24 2/2:48
NbLab330C06 30728018 NbLab3300177408 ? C,T 45.0 . DP=100;ANN=C|intergenic_region|MODIFIER|gene.49723.0-gene.49722.4|gene.49723.0-gene.49722.4|intergenic_region|gene.49723.0-gene.49722.4|||n.30728018?>C||||||,T|intergenic_region|MODIFIER|gene.49723.0-gene.49722.4|gene.49723.0-gene.49722.4|intergenic_region|gene.49723.0-gene.49722.4|||n.30728018?>T|||||| GT:DP 2/2:1 2/2:21 1/1:9 1/1:42/2:14 1/1:15 2/2:19 1/1:17

What did I miss?

Thank you in advance,

snpeff snps • 205 views
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Entering edit mode
6 weeks ago
cfos4698 ▴ 450

snpEff won't generate the html stats file unless you use the appropriate flag. Try:

snpEff eff -Xmx20G -s snpEff_stats.html LAB330 LabUsa16cWild01-20_L-Q.vcf > LabUsa16cWild01-20_L-Q.annotated.vcf

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Unfortunately, It still did not generate it.

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