Bioinformatics Recipe Cookbook

Run Parameters
Parameters used during the run:
  • Chromosomal Range: 1000000
Output Messages
Messages printed to the standard output stream:
file         format  type  num_seqs     sum_len  min_len  avg_len  max_len
reads/r1.fq  FASTQ   DNA    246,561  37,230,711      151      151      151
reads/r2.fq  FASTQ   DNA    246,555  37,229,805      151      151      151
Other Messages
Messages printed to the standard error stream:
+ mkdir -p reads
+ RANGE=18:1-1,000,000
+ UBAM=reads/chr18.bam
+ URL=ftp://ftp.sra.ebi.ac.uk/vol1/ERA596/ERA596280/bam/CHM1_CHM13_3.bam
+ samtools view -b ftp://ftp.sra.ebi.ac.uk/vol1/ERA596/ERA596280/bam/CHM1_CHM13_3.bam 18:1-1,000,000
+ rm -f CHM1_CHM13_3.bam.bai
+ R1=reads/r1.fq
+ R2=reads/r2.fq
+ samtools fastq -f 2 -1 reads/r1.fq -2 reads/r2.fq reads/chr18.bam
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 493116 reads
+ seqkit stat reads/r1.fq reads/r2.fq
+ mkdir -p ref
+ REF=ref/chr18.fa
+ GENOME_URL=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/chr18.fa.gz
+ curl -s http://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/chr18.fa.gz
+ gunzip -c
+ bwa index ref/chr18.fa
+ samtools faidx ref/chr18.fa
+ BAM=align18.bam
+ TAG='@RG\tID:1\tSM:CHM1_CHM13_3\tLB:Pond-482886'
+ bwa mem -t 4 -R '@RG\tID:1\tSM:CHM1_CHM13_3\tLB:Pond-482886' ref/chr18.fa reads/r1.fq
+ samtools sort -@ 4
[bam_sort_core] merging from 0 files and 4 in-memory blocks...
+ samtools index align18.bam
+ TRUTH_URL=https://github.com/lh3/CHM-eval/releases/download/v0.5/rep2.37.broad.hc.raw.vcf.gz
+ curl -sL https://github.com/lh3/CHM-eval/releases/download/v0.5/rep2.37.broad.hc.raw.vcf.gz
+ bcftools index ref/truth.vcf.gz
+ bcftools view ref/truth.vcf.gz 18
+ freebayes -f ref/chr18.fa -P .5 align18.bam
+ vt normalize -r ref/chr18.fa -
+ bcftools mpileup -Ou -B --min-MQ 40 -f ref/chr18.fa align18.bam
+ bcftools call -Ou -v -m -
+ bcftools norm -Ov -f ref/chr18.fa -d all
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[mpileup] 1 samples in 1 input files
Lines   total/split/realigned/skipped:	2563/0/359/0
+ picard CreateSequenceDictionary REFERENCE=ref/chr18.fa OUTPUT=ref/chr18.dict
+ /home/www/bin/gatk HaplotypeCaller -R ref/chr18.fa -I align18.bam -O align18.bam.gatk.vcf

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