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23 months ago
Pamella
•
0
Hello. I really need some help regarding the parameters of a VCF file. I made a denovo assembly with stacks, I don't have any reference genome for my object of study and I called SNPs. I was doing the filtering using the DP > 10 parameters, but when I saw the data in AD I noticed that in most lines the ALT value is 0. For example: AD:49.0 DP: 49 GL:-0.00,-14.98,-212.31 GQ:40 GT:0/0 REF/ALT:G/G NS:19 CROM:1228 POS:71 and in some AD=128,192; AD=10.8; AD=0.10. In these cases, what can I take into account? Better to filter by AD to be more reliable? And what is the ideal ratio of AD between REF and ALT? Could you use GL as well for filtering? How would you choose the best GL parameters? Thank you!
