Created
February 22, 2016 09:01
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#!/home/fng514/bin/julia | |
#$ -S /home/fng514/bin/julia | |
#$ -cwd | |
# Christian Theil Have, 2016. | |
#import GZip | |
function process_vcf_line(outfile,line, dpmin, gqmin) | |
fields = split(line) | |
# Find the index of genotype quality fields | |
#println(string(":>", fields[1:9])) | |
gtidx = first(find(x -> x=="GT", split(fields[9],':'))) | |
gqidx = first(find(x -> x=="GQ", split(fields[9],':'))) | |
dpidx = first(find(x -> x=="DP", split(fields[9],':'))) | |
removed = 0 | |
i = 1 | |
field_idx = 10 | |
for field in fields[10:end] | |
field_values = split(field,':') | |
gt = field_values[gtidx] | |
gq = field_values[gqidx] | |
dp = field_values[dpidx] | |
if gt != "./." | |
if (parse(Int,dp) < dpmin) || (gq != "." && parse(Int,gq) < gqmin) | |
field_values[gtidx] = "./." | |
removed += 1 | |
end | |
end | |
fields[field_idx] = join(field_values,":") | |
field_idx += 1 | |
end | |
#println(join(fields,"\t")) | |
write(outfile,string(join(fields,"\t"), "\n")) | |
return [fields[1], fields[2], fields[3], removed] | |
end | |
function process_vcf_line(outfile,line, dpmin) | |
fields = split(line) | |
# Find the index of genotype quality fields | |
gtidx = first(find(x -> x=="GT", split(fields[9],':'))) | |
dpidx = first(find(x -> x=="DP", split(fields[9],':'))) | |
removed = 0 | |
i = 1 | |
field_idx = 10 | |
for field in fields[10:end] | |
field_values = split(field,':') | |
gt = field_values[gtidx] | |
dp = field_values[dpidx] | |
if gt != "./." | |
if ((try parse(Int,dp) catch 0 end) < dpmin ) | |
field_values[gtidx] = "./." | |
removed += 1 | |
end | |
end | |
fields[field_idx] = join(field_values,":") | |
field_idx += 1 | |
end | |
#println(join(fields,"\t")) | |
write(outfile,string(join(fields,"\t"), "\n")) | |
return [fields[1], fields[2], fields[3], removed] | |
end | |
DP_threshold=20 | |
GQ_threshold=20 | |
outvcf = open(ARGS[2], "w") | |
bad_sites_file = open(string(ARGS[1], ".bad_sites.vcf"), "w") | |
open(ARGS[1]) do vcf | |
lines_read = 0 | |
line_refs = [] | |
removed_by_variant = [] | |
for line in eachline(vcf) | |
if ismatch(r"^chr", line) | |
try | |
push!(removed_by_variant,process_vcf_line(outvcf, line, DP_threshold, GQ_threshold)) | |
catch | |
push!(removed_by_variant,process_vcf_line(outvcf, line, DP_threshold)) | |
write(bad_sites_file, line) | |
end | |
else | |
write(bad_sites_file, line) | |
write(outvcf,line) | |
end | |
lines_read += 1 | |
if lines_read % 10 == 0 | |
println(lines_read) | |
end | |
end | |
open(string(ARGS[2], "_summary_dpgq"), "w") do outfile | |
for v in removed_by_variant | |
write(outfile,string(join(v,"\t"),"\n")) | |
end | |
end | |
end | |
close(bad_sites_file) | |
close(outvcf) |
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