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修改血液的过滤条件

master
chaopower 2023-12-28 10:53:53 +08:00
parent 493a99cecd
commit a48795ac8b
1 changed files with 13 additions and 6 deletions
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17
codes/filter_snpindel.pl
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@ -84,13 +84,13 @@ while (<IN>) {
push @reason, 'benign';
}
# 不是pass 低频的； 或者 0.02 < 0.05 之间 个数大于2
if ($line[101] ne 'PASS' and ($freq < 0.02 or ($freq >= 0.02 and $freq < 0.05 and $filters >= 2))) {
# cfdna 样本
if ($sample_type eq 'c') {
if ($line[101] ne 'PASS' and ($freq < 0.005 or ($freq >= 0.005 and $freq < 0.01 and $filters >= 2))) {
push @reason, 'byfilter';
}
# cfdna 样本
if ($sample_type eq 'c') {
# 低频的 cosmic91 无记录的
if ($freq < 0.01 and $line[11] eq '.') {
push @reason, 'cfdna_lowfreq_cosmic';
@ -110,6 +110,13 @@ while (<IN>) {
}
}
}
else {
# 不是pass 低频的； 或者 0.02 < 0.05 之间 个数大于2 血液 0.005 - 0.01
if ($line[101] ne 'PASS' and ($freq < 0.02 or ($freq >= 0.02 and $freq < 0.05 and $filters >= 2))) {
push @reason, 'byfilter';
}
}
my $protein;
if ($line[9] eq '.') {
@ -139,7 +146,7 @@ while (<IN>) {
else {
push @reason, 'not_need_spl';
}
if ($gene eq "MET" ) {
if ($gene eq "MET") {
$line[9] = join(":", ($gene, "NM_000245", "exon14", "c.xxx"));
$line[8] = 'skipping'
}