Hi,

I wanted to generate consenus sequence for PSMC analysis. I have a bam file. But, fpr PSMC analysis they said we need to generate diploid sequence. It means I need to use 2n=34 chromosome genome? or n=17 chromosome genome assembly? if n=34, should I index it? If my question seems stupid then excuse me :). Here is my command:

samtools mpileup -C50 -uf ./ref.fasta ./bams/DHB109B.sort.rmdup.bam |  bcftools view -c - \
      | vcfutils.pl vcf2fq -d 10 -D 100 | gzip > diploid_DHB109B.fq.gz