Entering edit mode
6.8 years ago
cristina_sabiers ▴ 110
well finally I got my snps with added gen...of course a lot of extra information like....
chr1 14815 0 C T 0.00012928 0 AB=0 ABP=0 AC=0 AF=0 AN=2 AO=3 CIGAR=1X DP=14 DPB=14 DPRA=0 EPP=3.73412 EPPR=7.94546 GTI=0 LEN=1 MEANALT=1 MQM=6 MQMR=8.27273 NS=1 NUMALT=1 ODDS=10.4802 PAIRED=0 PAIREDR=0 PAO=0 PQA=0 PQR=0 PRO=0 QA=77 QR=242 RO=11 RPL=1 RPP=3.73412 RPPR=4.78696 RPR=2 RUN=1 SAF=3 SAP=9.52472 SAR=0 SRF=5 SRP=3.20771 SRR=6 TYPE=snp technology.IONTORRENTIon=1 GENE=WASH7P GT:DP:DPR:RO:QR:AO:QA:GL 0/0:14:14 3:11:242:3:77:0 -2.55149 -5.77448
Now what I want is to compare for example in a family having the xls from each individual, which snps they share(same position, same base) and make my own tables, as well to be able to generate a report with the info of the genes which are in common (just as sample). I dont know if is better work directly with vcf files or my snps calls xls table.
Any ideas how I can start looking?
If you want to know the intersect between two vcf file "shared between two samples for examples" you can use bedtools ,
for comparing you can also use SnpSift Concordance also it contains a lot of features that could help you also can use VCFtools
Thanks a lot medhat! :)))