Hi, I was wondering what tool I could use to annotate a vcf and include the two flanking bases, upstream and downstream of each SNP. Ideally I would like to get a count table such as the one from SnpEff when the csvStats option is used, but including three nucleotides instead of just one. At first I thought SnpEff's --upDownStreamLen argument was it, but as far as I'm concerned this is just to define the 'upstream/downstream effect' zone. Thanks in advance.
Question: Annotating the two flanking bases of SNPs in a VCF file (perhaps SnpEff?)
3.8 years ago by
lm687 • 50
lm687 • 50 wrote:
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3.8 years ago by
Pierre Lindenbaum ♦ 134k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 134k wrote:
I've quickly written something: http://lindenb.github.io/jvarkit/Biostar251649.html
$ java -jar dist/biostar251649.jar -n 10 -R tests/ref.fa tests/mutations.vcf ##INFO=<ID=SEQ3_10,Number=1,Type=String,Description="Sequence on the 3' of mutation"> ##INFO=<ID=SEQ5_10,Number=1,Type=String,Description="Sequence on the 5' of mutation"> (...) #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 S2 S3 S4 rotavirus 51 . A G 22.55 . AC1=2;AF1=0.25;BQB=1;DP=944;DP4=849,0,93,0;FQ=23.7972;G3=0.75,0,0.25;HWE=0.033921;MQ=60;MQ0F=0;MQB=1;PV4=1,1,1,1;RPB=0.993129;SEQ3_10=GATGGTAAGC;SEQ5_10=TCTACTCAGC;SGB=-61.9012;VDB=3.53678e-05 GT:PL 0/0:0,255,134 0/0:0,255,127 0/0:0,255,137 1/1:70,255,0 rotavirus 91 . A T 5.45 . AC1=1;AF1=0.124963;BQB=0.951201;DP=1359;DP4=1134,0,225,0;FQ=5.8713;MQ=60;MQ0F=0;MQB=1;PV4=1,4.80825e-05,1,1;RPB=0.0393173;SEQ3_10=GTTGTTGCTG;SEQ5_10=TTGAAGCTGC;SGB=-369.163;VDB=0.313337 GT:PL 0/0:0,255,133 0/1:40,0,31 0/0:0,255,134 0/0:0,255,82
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