Hi,
I use genomicSuperDups,1000g2012apr_all,
snp137NonFlagged,snp137,dgv for filtering variants. But when I use them to select variants that are in 2kb downstream/upstream of tbfs, they remove almost all variants except 10. Most of the variants are removed by genomicSuperDups.
On the other hand, when I use these filtering criteria to select non-coding variants, at the end, around 200 are remained.
Do you have any filtering suggestion that could be less stringent for the tbfs case (to remove fewer) and additional criteria that could be applied to the other case to reduce the number of variants?
BW
I use genomicSuperDups,1000g2012apr_all,
snp137NonFlagged,snp137,dgv for filtering variants. But when I use them to select variants that are in 2kb downstream/upstream of tbfs, they remove almost all variants except 10. Most of the variants are removed by genomicSuperDups.
On the other hand, when I use these filtering criteria to select non-coding variants, at the end, around 200 are remained.
Do you have any filtering suggestion that could be less stringent for the tbfs case (to remove fewer) and additional criteria that could be applied to the other case to reduce the number of variants?
BW