Filetering low reads from vcf file/ download exonic region, coding regions of GRCh38 - hg38

Question

[minoo]

I am analyzing variant calling on RNASeq data using somatic pipeline of mutect2 function in gatk. To fileter the resulting variants, I need to filter out low reads in a way that for example the sum of reads from ref and alt be more than 50. Like here:

0/1:4,21:25:64:615,0,64 4+21<50 so this variants needs to be omitted. Do you have any idea how to do it?

Also I need to remove noncoding variants from this vcf file as it is coming from RNaseq data. I need a bedfile including exonic region and coding regions to be able to filter out noncoding variants. Do you know where can I get such a file? I tried the UCSC website but I could not figure out the position criteria to get such a bed file.

Answer 1

[Pierre Lindenbaum]

assuming FORMAT/AD[0]+FORMAT/AD[1] == FORMAT/DP

bcftools view -i 'FORMAT/DP >= 50'  in.vcf

I need a bedfile including exonic region and coding regions

get a GTF file, filter for exon/transcript with awk, convert to bed with awk, use bedtools merge followed by bedtools complement to get the BED for the non-coding genome.

[minoo]

Thanks Pierre, I will try that. Do you think the above threshold can replace the filtering function from picard :

java -jar $picardTool FilterVcf \
 -I input.vcf \
 -O output.vcf \
 --MIN_DP 50

for the second part of my question, how should I do this filtering? I tried using the code below

wget -O - "http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/gencode.v43.annotation.gtf.gz" |\
gunzip -c | grep 'transcript_type "protein_coding"' |\
awk '($3=="exon") {printf("%s\t%s\t%s\n",$1,int($4)-1,$5);}' |\
sort -T . -t $'\t' -k1,1 -k2,2n | bedtools merge > coding.regions.hg38.bed

replacing 'transcript_type "protein_coding"' with 'exon "transcript"' but it didnt work. Do you think the above code will output the coding region wwithout specifying the exon/transcripts?