Nitin Ravikanthachari nitinra

## genome_oneliners.md

      
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                nitinra
                / genome_oneliners.md
            
            
              Created
              October 25, 2022 12:09
                — forked from darencard/genome_oneliners.md
            
              
                Quick one-liner commands that are useful for genomics
              
          
    Useful Genomics Oneliners

The following commands sometimes require non-standard software like bioawk and seqtk.
rename scaffold headers with sequential numbers and lengths ("scaffold-N ")
bioawk -c fastx '{ print ">scaffold-" ++i" "length($seq)"\n"$seq }' < genome.fasta > new_genome.fasta
make association table of old and renamed scaffold names after above renaming command

  
## lumpy_cnvnator.sh
WIN=100
SAMPLE="NA12878"
SAMPLE_BAM="NA12878_S1.bam"

cnvnator -root $SAMPLE.$WIN.root -genome GRCh37 -tree $SAMPLE_BAM
cnvnator -genome GRCh37 -root $SAMPLE.$WIN.root -his $WIN -d /shared/genomes/b37/full/chroms
cnvnator -root $SAMPLE.$WIN.root -stat $WIN
cnvnator -root $SAMPLE.$WIN.root -partition $WIN
cnvnator -root $SAMPLE.$WIN.root -call $WIN > $SAMPLE.$WIN.cnvcalls.txt
	WIN=100
	SAMPLE="NA12878"
	SAMPLE_BAM="NA12878_S1.bam"

	cnvnator -root $SAMPLE.$WIN.root -genome GRCh37 -tree $SAMPLE_BAM
	cnvnator -genome GRCh37 -root $SAMPLE.$WIN.root -his $WIN -d /shared/genomes/b37/full/chroms
	cnvnator -root $SAMPLE.$WIN.root -stat $WIN
	cnvnator -root $SAMPLE.$WIN.root -partition $WIN
	cnvnator -root $SAMPLE.$WIN.root -call $WIN > $SAMPLE.$WIN.cnvcalls.txt