outPut.sam is my sam file from bowtie2.
I am trying to generate a consensus fq/fasta file from it.
I ran:
Now when I try to use this command:
samtools-1.1/./samtools mpileup -uf sequence.fasta sorted_bam.bam.bam | bcftools/./bcftools view -cg - | bcftools/./vcfutils.pl vcf2fq > cns.fq
I get an error,
Error: Could not parse --min-ac g
[mpileup] 1 samples in 1 input files
Use of uninitialized value $l in numeric lt (<) at bcftools/./vcfutils.pl line 566.
Use of uninitialized value $l in numeric lt (<) at bcftools/./vcfutils.pl line 566.
<mpileup> Set max per-file depth to 8000
And everything stops.
It is something with bcftools.
References:
Please guide.
I am trying to generate a consensus fq/fasta file from it.
I ran:
samtools-1.1/./samtools view -bS outPut.sam > bamOut.bam --> get the bam file out of sam file
samtools-1.1/./samtools sort bamOut.bam sorted_bam.bam --> sort the bam file
samtools-1.1/./samtools index sorted_bam.bam.bam --> create the index of the bam file sorted
samtools-1.1/./samtools sort bamOut.bam sorted_bam.bam --> sort the bam file
samtools-1.1/./samtools index sorted_bam.bam.bam --> create the index of the bam file sorted
samtools-1.1/./samtools mpileup -uf sequence.fasta sorted_bam.bam.bam | bcftools/./bcftools view -cg - | bcftools/./vcfutils.pl vcf2fq > cns.fq
I get an error,
Error: Could not parse --min-ac g
[mpileup] 1 samples in 1 input files
Use of uninitialized value $l in numeric lt (<) at bcftools/./vcfutils.pl line 566.
Use of uninitialized value $l in numeric lt (<) at bcftools/./vcfutils.pl line 566.
<mpileup> Set max per-file depth to 8000
It is something with bcftools.
References:
Please guide.
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