IGV batch screenshots about viralrecon HOT 3 CLOSED

Where is this happening in the workflow? I wonder if https://github.com/bigdatagenomics/mango might be able to help.

from viralrecon.

An alternative solution to this would be asciigenome too. Maybe a command like the below would do the trick:

• Get a list of variants in BED format from the VCF file and pad by 50bp either side to zoom out a little

zcat TOL743A312592_S192_L001.vcf.gz | grep -v '#' | awk -v FS='\t' -v OFS='\t' '{print $1, ($2-50), ($2+50+1)}' > batch.txt

• Run ASCIIGenome

ASCIIGenome -ni -x "trackHeight 25 && readsAsPairs -on && save TOL743A312592_S192_L001.%r.pdf" --batchFile batch.txt --fasta MN908947.3.fa TOL743A312592_S192_L001.ivar_trim.sorted.bam TOL743A312592_S192_L001.vcf.gz > /dev/null

from viralrecon.

Added ASCIIGenome for its awesome batch processing more here #186

from viralrecon.