Empty result obtained when using SAMTOOLS and MPILEUP to generate consensus sequences FASTQ file
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?
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roelofco •
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