Masking fastq file for repeats
Hello,
I am using the PSMC pipeline as follows:
samtools mpileup -C50 -uf reference individual | \
bcftools call -c | vcfutils.pl vcf2fq -d 10 -D 100 | \
gzip > out.fastq
fq2psmcfa -q20 out.fastq > psmc.fa
I would like to use a bed file with repeat and gene coordinates to mask these features from the out.fastq file used as an input for fq2psmcfa. Is there any way that I could achieve this?
Thank you!
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I've added the
psmctag to this post. Given that it's an important part of the question, you should have added the tag at creation, thjnant.