Annotating the two flanking bases of SNPs in a VCF file (perhaps SnpEff?)

Question

[lm687]

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.

Answer 1

[Pierre Lindenbaum]

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

[lm687]

Thank you so much, I will use it now! My solution was to do

b=`grep -v '#'  SAMPLE.vcf | awk '{print $1":"($2 - 1)"-"($2+1)}'`; for i in $b; do samtools faidx genome.fa $i; done

(the potential problem of which being when two SNPs appear consecutively)