Quite new to command line for NGS data analysis… on steep learning curve and loving it so far
Developing a pipeline and stuck.
Mapping to reference: when there are some areas of no coverage how can I include reference sequence in the consensus rather than Ns’s… to then use this consensus as reference file.
Using bowtie2, bcftools mpileup, bcftools call -c and a modified version of vcf2fq.
Have tried a number of options but no success so far.
Any advice would be very much appreciated.
Developing a pipeline and stuck.
Mapping to reference: when there are some areas of no coverage how can I include reference sequence in the consensus rather than Ns’s… to then use this consensus as reference file.
Using bowtie2, bcftools mpileup, bcftools call -c and a modified version of vcf2fq.
Have tried a number of options but no success so far.
Any advice would be very much appreciated.
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