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#!/software/bin/python
# Author: lh3, converted to python and modified to add -C option by Aylwyn Scally
#
# About:
# varfilter.py is a port of Heng's samtools.pl varFilter script into
# python, with an additional -C INT option. This option sets a minimum
# consensus score, above which the script will output a pileup line
# wherever it _could have_ called a variant, even if none is actually
# called (i.e. hom-ref positions). This is important if you want to
# subsequently merge the calls with those for another individual to get a
# synoptic view of calls at each site. Without this option, and in all
# other respects, it behaves like samtools.pl varFilter.
#
# Aylwyn Scally as6@sanger.ac.uk
# Filtration code:
#
# C low CNS quality (hom-ref only)
# d low depth
# D high depth
# W too many SNPs in a window (SNP only)
# G close to a high-quality indel (SNP only)
# Q low RMS mapping quality (SNP only)
# g close to another indel with higher quality (indel only)
# s low SNP quality (SNP only)
# i low indel quality (indel only)
import sys
import getopt
def usage():
print '''usage: varfilter.py [options] [cns-pileup]
Options: -Q INT minimum RMS mapping quality for SNPs
-q INT minimum RMS mapping quality for gaps
-d INT minimum read depth
-D INT maximum read depth
-S INT minimum SNP quality
-i INT minimum indel quality
-C INT minimum consensus quality for hom-ref sites
-G INT min indel score for nearby SNP filtering
-w INT SNP within INT bp around a gap to be filtered
-W INT window size for filtering dense SNPs
-N INT max number of SNPs in a window
-l INT window size for filtering adjacent gaps
-p print filtered variants'''
def varFilter_aux(first, is_print):
try:
if first[1] == 0:
sys.stdout.write("\t".join(first[4:]) + "\n")
elif is_print:
sys.stderr.write("\t".join(["UQdDWGgsiCX"[first[1]]] + first[4:]) + "\n")
except IOError:
sys.exit()
mindepth = 3
maxdepth = 100
gapgapwin = 30
minsnpmapq = 25
mingapmapq = 10
minindelscore = 25
scorefactor = 100
snpgapwin = 10
densesnpwin = 10
densesnps = 2
printfilt = False
minsnpq = 0
minindelq = 0
mincnsq = 0
try:
options, args = getopt.gnu_getopt(sys.argv[1:], 'pq:d:D:l:Q:w:W:N:G:S:i:C:', [])
except getopt.GetoptError:
usage()
sys.exit(2)
for (oflag, oarg) in options:
if oflag == '-d': mindepth = int(oarg)
if oflag == '-D': maxdepth = int(oarg)
if oflag == '-l': gapgapwin = int(oarg)
if oflag == '-Q': minsnpmapq = int(oarg)
if oflag == '-q': mingapmapq = int(oarg)
if oflag == '-G': minindelscore = int(oarg)
if oflag == '-s': scorefactor = int(oarg)
if oflag == '-w': snpgapwin = int(oarg)
if oflag == '-W': densesnpwin = int(oarg)
if oflag == '-C': mincnsq = int(oarg)
if oflag == '-N': densesnps = int(oarg)
if oflag == '-p': printfilt = True
if oflag == '-S': minsnpq = int(oarg)
if oflag == '-i': minindelq = int(oarg)
if len(args) < 1:
inp = sys.stdin
else:
inp = open(args[0])
# calculate the window size
max_dist = max(gapgapwin, snpgapwin, densesnpwin)
staging = []
for t in (line.strip().split() for line in inp):
(flt, score) = (0, -1)
# non-var sites
if t[3] == '*/*':
continue
is_snp = t[2].upper() != t[3].upper()
if not (is_snp or mincnsq):
continue
# clear the out-of-range elements
while staging:
# Still on the same chromosome and the first element's window still affects this position?
if staging[0][4] == t[0] and int(staging[0][5]) + staging[0][2] + max_dist >= int(t[1]):
break
varFilter_aux(staging.pop(0), printfilt)
# first a simple filter
if int(t[7]) < mindepth:
flt = 2
elif int(t[7]) > maxdepth:
flt = 3
if t[2] == '*': # an indel
if minindelq and minindelq > int(t[5]):
flt = 8
elif is_snp:
if minsnpq and minsnpq> int(t[5]):
flt = 7
else:
if mincnsq and mincnsq > int(t[4]):
flt = 9
# site dependent filters
dlen = 0
if flt == 0:
if t[2] == '*': # an indel
# If deletion, remember the length of the deletion
(a,b) = t[3].split('/')
alen = len(a) - 1
blen = len(b) - 1
if alen>blen:
if a[0] == '-': dlen=alen
elif b[0] == '-': dlen=blen
if int(t[6]) < mingapmapq:
flt = 1
# filtering SNPs
if int(t[5]) >= minindelscore:
for x in (y for y in staging if y[3]):
# Is it a SNP and is it outside the SNP filter window?
if x[0] >= 0 or int(x[5]) + x[2] + snpgapwin < int(t[1]):
continue
if x[1] == 0:
x[1] = 5
# calculate the filtering score (different from indel quality)
score = int(t[5])
if t[8] != '*':
score += scorefactor * int(t[10])
if t[9] != '*':
score += scorefactor * int(t[11])
# check the staging list for indel filtering
for x in (y for y in staging if y[3]):
# Is it a SNP and is it outside the gap filter window
if x[0] < 0 or int(x[5]) + x[2] + gapgapwin < int(t[1]):
continue
if x[0] < score:
x[1] = 6
else:
flt = 6
break
else: # a SNP or hom-ref
if int(t[6]) < minsnpmapq:
flt = 1
# check adjacent SNPs
k = 1
for x in (y for y in staging if y[3]):
if x[0] < 0 and int(x[5]) + x[2] + densesnpwin >= int(t[1]) and (x[1] == 0 or x[1] == 4 or x[1] == 5):
k += 1
# filtering is necessary
if k > densesnps:
flt = 4
for x in (y for y in staging if y[3]):
if x[0] < 0 and int(x[5]) + x[2] + densesnpwin >= int(t[1]) and x[1] == 0:
x[1] = 4
else: # then check gap filter
for x in (y for y in staging if y[3]):
if x[0] < 0 or int(x[5]) + x[2] + snpgapwin < int(t[1]):
continue
if x[0] >= minindelscore:
flt = 5
break
staging.append([score, flt, dlen, is_snp] + t)
# output the last few elements in the staging list
while staging:
varFilter_aux(staging.pop(0), printfilt)
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