Description
Hello, I am using smoove to call SV. Some of the information in the output file it produces makes me confused. I asked brentp and he told me that the information comes from svtyper. Therefore, I hope you can help me out.
Look at a record:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 256T_S8_L002 256N_S7_L002
chr3 41224322 324 N 63802.1. SVTYPE=DEL;SVLEN=-607;END=41224929;STRANDS=+-:1875;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0 ,0; SU=1875;PE=799;SR=1076;PRPOS=1;PREND=1;AC=1;AN=4 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS: AS:ASC :RP:AP:AB 0/1:200:63802.1:-6528,-148,-3091:8245:5290:2954:5289:2953:2924:1079:328:2365:1546:0.36 0/0:200: 0:-2,-3029,-10093:10113:10108:5:10107:4:5538:1:0:4569:2:0.0004
problem:
1.Shouldn't DP be the sum of AO and RO? Why is AO+RO always 1 smaller than DP?
2.What exactly does QR, QA, RS, AS, ASC, RP, AP mean? Can you explain it based on the record above?
3. How should I calculate the Variant allele frequency of the tumor? AO/DP?
4.if I want to get a variation with the frequency greater than 0.2 in the tumor and less than 0.01 in the paired normal sample, What should I do?
Thanks a lot
Tang