Bioinformatics Recipe Cookbook

Run Parameters
Parameters used during the run:
  • Accession number for the reference genome: AF086833
  • SRA run number: SRR1972739
Output Messages
Messages printed to the standard output stream:
Read 10000 spots for SRR1972739
Written 10000 spots for SRR1972739
Other Messages
Messages printed to the standard error stream:
+ ACC=AF086833
+ SRR=SRR1972739
+ mkdir -p refs
+ GB=refs/AF086833.gb
+ REF=refs/AF086833.fa
+ GFF=refs/AF086833.gff
+ efetch -db=nuccore -format=gb -id=AF086833
+ cat refs/AF086833.gb
+ readseq -p -f fasta
+ readseq -p -f gff
+ grep CDS
+ cat refs/AF086833.gb
+ bwa index refs/AF086833.fa
+ samtools faidx refs/AF086833.fa
+ mkdir -p reads
+ fastq-dump -X 10000 --split-files -O reads SRR1972739
+ R1=reads/SRR1972739_1.fastq
+ R2=reads/SRR1972739_2.fastq
+ BAM=SRR1972739.bam
+ VCF=SRR1972739.vcf
+ bwa mem refs/AF086833.fa reads/SRR1972739_1.fastq reads/SRR1972739_2.fastq
+ samtools sort
+ samtools index SRR1972739.bam
+ bcftools mpileup -Ou -f refs/AF086833.fa SRR1972739.bam
+ bcftools call -mv -Ov -o SRR1972739.vcf

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