Entering edit mode
4.5 years ago
roelofco
▴
10
Hi Everyone!!
In the past I have had great success when extracting consensus sequences from BAM files when generated using bowtie2. This I do as the following:
samtools \
mpileup \
-uf \
output.bam | bcftools call -c | vcfutils.pl vcf2fq > consensus_sequences.fastq
However, recently I have been working on mapping some sequences that result in very low coverage and gaps between consensus sequences. Despite this I still need to extract any consensus sequences in FASTQ format.
The result I have been getting is an empty FASTQ file with only @+ in the top two lines.
Does anyone have any suggestions on how I can extract consensus sequences from these resulting BAM files?
