Samtools Error: Creating a Consensus fastq Sequence from Bam File

Question

[eden.maloney]

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

[madkitty]

You posted twice that question, please delete one.

[eden.maloney]

Sorry! will do!

[eden.maloney]

-d8000 fixes: <mpileup> Set max per-file depth to 8000

Answer 1

[eden.maloney]

Converting Bam to Fastq

bwa index -a bwtsw 1000.fasta
bwa aln 1000.fasta ERR244000_1.fastq > aln_sa1b.sai
bwa aln 1000.fasta ERR244000_2.fastq > aln_sa2b.sai
bwa sampe 1000.fasta aln_sa1b.sai aln_sa2b.sai ERR244000_1.fastq ERR244000_2.fastq > readset_refb_bwa.sam
samtools view -bS -o readset_refb_bwa.bam readset_refb_bwa.sam
samtools sort readset_refb_bwa.bam readset_refb_bwa.sorted
samtools index readset_refb_bwa.sorted.bam
samtools mpileup -d8000 -uf 1000.fasta readset_refb_bwa.sorted.bam | bcftools call -c | vcfutils.pl vcf2fq > cnsnew.fq