PSMC分析流程

bowtie2-build ../genome.fasta genome
bowtie2 -x genome -p 80 -1 reads.1.fastq -2 reads.2.fastq -S bowtie2.sam
samtools sort -o bowtie2_sort.bam -O BAM -@ 40 -m 4G bowtie2.sam
/opt/biosoft/samtools-0.1.18/samtools mpileup -C50 -uf ../genome.fasta bowtie2_sort.bam > gc_psmc.bcf
/opt/biosoft/samtools-0.1.18/bcftools/bcftools view -c gc_psmc.bcf > Pb_2G.vcf
vcfutils.pl vcf2fq -d 10 -D 100 Pb_2G.vcf | gzip > diploid.fq.gz
/opt/biosoft/psmc-master/utils/fq2psmcfa -q20 diploid.fq.gz > diploid.psmcfa
/opt/biosoft/psmc-master/utils/splitfa diploid.psmcfa > split.psmcfa
/opt/biosoft/psmc-master/psmc -N25 -t15 -r5 -p "4+25*2+4+6" -o diploid.psmc diploid.psmcfa
seq 100 | xargs -i echo /opt/biosoft/psmc-master/psmc -N25 -t15 -r5 -b -p "4+25*2+4+6" -o round-{}.psmc split.fa | sh
cat diploid.psmc round-*.psmc > combined.psmc
/opt/biosoft/psmc-master/utils/psmc_plot.pl -g x -u y combined combined.psmc
# x为该物种繁殖一代的时间，比如人的默认为25年，该处值为-g 25.
# y为该物种碱基替换率，可由进化树的枝长除以r8s评估该物种的分歧时间得到