jodyphelan · May 4, 2018 08:27
diff --git a/new test b/new test
 export THREADS=40

 time python filter_out_large_del_reads.py  
 time seqtk subseq SRR6117388.sampled.fastq.gz test.filtered_read_names.txt | pigz -c > filtered_reads.fastq.gz
 ./minimap2/minimap2 -t $THREADS -R '@RG\tID:test\tSM:test\tPL:minION' -a -x map-ont H37Rv.fa filtered_reads.fastq.gz| ./samtools-1.8/samtools view -@ $THREADS -b - | ./samtools-1.8/samtools view -F 2048 - | ./samtools-1.8/samtools sort -@ $THREADS -o filtered.bam -
 samtools index -@ $THREADS filtered.bam 
 splitchr.py H37Rv.fa 50000 --reformat | parallel --col-sep '\t' "./bcftools-1.8/bcftools mpileup -f H37Rv.fa filtered.bam -B -Q8 -a AD -r {1} | ./bcftools-1.8/bcftools call -mv -o filtered.{2}.bcf -Ob "
	export THREADS=40

	time python filter_out_large_del_reads.py
	time seqtk subseq SRR6117388.sampled.fastq.gz test.filtered_read_names.txt \| pigz -c > filtered_reads.fastq.gz
	./minimap2/minimap2 -t $THREADS -R '@RG\tID:test\tSM:test\tPL:minION' -a -x map-ont H37Rv.fa filtered_reads.fastq.gz\| ./samtools-1.8/samtools view -@ $THREADS -b - \| ./samtools-1.8/samtools view -F 2048 - \| ./samtools-1.8/samtools sort -@ $THREADS -o filtered.bam -
	samtools index -@ $THREADS filtered.bam
	splitchr.py H37Rv.fa 50000 --reformat \| parallel --col-sep '\t' "./bcftools-1.8/bcftools mpileup -f H37Rv.fa filtered.bam -B -Q8 -a AD -r {1} \| ./bcftools-1.8/bcftools call -mv -o filtered.{2}.bcf -Ob "