Masking fastq file for repeats

Question

[thjnant]

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!

[Ram]

I've added the psmc tag to this post. Given that it's an important part of the question, you should have added the tag at creation, thjnant.