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Old 08-26-2019, 05:54 AM   #1
skylark
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Default How to include reference sequence instead of Nís in consensus

Quite new to command line for NGS data analysisÖ 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 NsísÖ 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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Old 08-26-2019, 09:17 PM   #2
finswimmer
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