Question: How to filter SNP and Indel data
1
ppurkayastha2010 • 30 wrote:
I have mapped my sequence with a wild type sequence using Bowtie2 and obtained around 8000 SNPs and 700 Indels using Varscan. Please let me know how do I further shortlist the SNPs and Indels (based on which criteria)?
The output file looks like this
POS #CHROM ID REF ALT QUAL FILTER INFO FORMAT Sample1
1 CP009494.1 . A C . PASS ADP=16;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:16:16:2:11:68.75%:9.8E-1:32:32:2:0:11:0
2 CP009494.1 . A G . PASS ADP=20;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:21:20:6:7:35%:9.8E-1:30:32:6:0:7:0
3 CP009494.1 . A G . PASS ADP=21;WT=0;HET=1;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/1:0:21:21:10:8:36.36%:9.8E-1:30:32:10:0:8:0
Now based on which criteria shall I shortlist the SNPs to a smaller number?? based on reads?
ADD COMMENT
• link
•
modified 20 months ago
by
Guy Reeves • 1.0k
•
written
20 months ago by
ppurkayastha2010 • 30
