跟着nature plants做种群历推断：PSMC、SMC++、MSMC2 (二)

https://datadryad.org/stash/share/jcQfZcbai80MmLb6kO4_mrQLfu1tX-I_1_Yx7hAfJkI

  1. ref=genome.fa

PSMC

  1. bcftools mpileup \
  2.   -C 50 \
  3.   -O u \
  4.   -f ${ref} \
  5.   ${bam} \
  6.   | bcftools call -c -Ov - \
  7.   | vcfutils.pl vcf2fq -d 10 -D 100 \
  8.   > ${sample}.fq
  11. fq2psmcfa -q 20 ${sample}.fq > ${sample}.psmcfa
  13. psmc \
  14.   -N 25 \
  15.   -t 15 \
  16.   -r 5 \
  17.   -p "4+25*2+4+6" \
  18.   -o ${sample}.psmc \
  19.   ${sample}.psmcfa
  1. splitfa ${sample}.psmcfa > ${sample}.split.psmcfa
  3. mkdir ${sample}.bootstrap
  5. for i in `seq 100`
  6. do
  7. psmc \
  8.   -N 25 \
  9.   -t 15 \
  10.   -r 5 \
  11.   -b \
  12.   -p "4+25*2+4+6" \
  13.   -o ${sample}.bootstrap/round-${i}.psmc \
  14.   e.${sample}.split.psmcfa
  15. done
  18. cat ${sample}.psmc ${sample}.bootstrap/round-*.psmc > ${sample}.addboot.psmc

SMC++

参考