#maximal read length
max_rd_len=

[LIB]

avg_ins=450

#if sequence needs to be reversed

reverse_seq=0

#in which part(s) the reads are used

asm_flags=3

#use only first 100 bps of each read

rd_len_cutoff=100

#in which order the reads are used while scaffolding
rank=1

# cutoff of pair number for a reliable connection (at least 3 for short insert size)

pair_num_cutoff=

#minimum aligned length to contigs for a reliable read location (at least 32 for short insert size)
map_len=32
#a pair of fastq file, read 1 file should always be followed by read 2 file

q1=../../data/newBGIseq500_1.fq.gz

q2=../../data/newBGIseq500_2.fq.gz

/home/stu2/Software/Assemblathon1_pipeline/SOAPdenovo-63mer_v2. all -s  asm.cfg -K  -p  -R -o asm >cout.log >cerr.log

./SOAPdenovo-63mer_v2. pregraph -K  -s asm.cfg -o asm -p  >pregraph.log >pregraph.err

./SOAPdenovo-63mer_v2. contig -s asm.cfg -g asm -M  -e  -p  -R -D   >contig.log >contig.err

./SOAPdenovo-63mer_v2. map -s asm.cfg -g asm -k  -p  >map.log >map.err

./SOAPdenovo-63mer_v2. scaff -g asm -p   -F >scaff.log >scaff.err

# get Qual

./vcftools --gzvcf chr17.vcf.gz --site-quality --out Qual

# get interval

./vcftools --gzvcf chr17.vcf.gz --chr chr17 --from-bp  --to-bp  --remove-indels --out TP53 --recode

#!/usr/bin/perl

use strict;

my $file = shift;

open(In,"gzip -dc $file|") or die ("can't open the file!\n");

my @type;

my @array = ( );

while(<In>){

   chomp;

   next if (/^##/);

   if (/^#/){

     my @line = split;

     push @type, $line[];

     push @type, $line[];

     push @type, $line[];

     next;

   }

   my @line = split;

   if ($line[] >= && $line[] <= && $line[] ne "."){

       my @type1 = split(/\/|:/, $line[]);

       my @type2 = split(/\/|:/, $line[]);

       my @type3 = split(/\/|:/, $line[]);

       #print "$type1[0]\t$type1[1]\n";

       if ($type1[]==$type1[]){

          $array[][] ++;

       }else{

          $array[][] ++;

       }

       if ($type2[] == $type2[]){

           $array[][] ++;

       }else{

           $array[][] ++;

       }

       if($type3[] == $type3[]){

           $array[][] ++;

       }else{

           $array[][] ++;

        }

   }

}

close IN;

print "Sample\tHomozygous\tHeterozygote\n";

print "$type[0]: $array[0][0]\t$array[0][1]\n";

print "$type[1]: $array[1][0]\t$array[1][1]\n";

print "$type[2]: $array[2][0]\t$array[2][1]\n";

./kmerfreq -k  -l lib.list -t  >17mer.freq >17mer.log

 reads1.fq.gz

 reads2.fq.gz