Entering edit mode
9.6 years ago
eden.maloney
▴
10
Hi Everyone,
I am a n00b to CS and I need really explicit instructions on how to fix this code. Thank you for your time!
I used these two tutorials:
- http://samtools.sourceforge.net/mpileup.shtml
- Reference Assembly - Mapping Reads To A Reference Genome
To Create this Code:
samtools mpileup -uf B95.8\ Reference\ Genome.fasta test.sorted.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cnsWIN.fq
And I am getting these errors:
Error: Could not parse --min-ac g
[mpileup] 1 samples in 1 input files
Use of uninitialized value $l in numeric lt (<) at /Users/Eden/Library/bcftools-1.2/vcfutils.pl line 566.
Use of uninitialized value $l in numeric lt (<) at /Users/Eden/Library/bcftools-1.2/vcfutils.pl line 566.
<mpileup> Set max per-file depth to 8000
You posted twice that question, please delete one.
Sorry! will do!
-d8000
fixes:<mpileup> Set max per-file depth to 8000