Hi :
I use samtools and bcftools to generate consensus sequence with reads bam
file, reference genome and VCF file:
samtools mpileup -vf reference.fasta reads.bam | bcftools call -m -O z - >
reads.vcf.gz
bcftools index reads.vcf.gz
bcftools consensus -f reference.fasta reads.vcf.gz -o consensus.fast
However, I found out the gap regions were filled with reference sequence
and I want to replace these gap sequences with "N",
For example:
Reference: AGTCTGG TTAA GGCTGCReads bam: . . . T . . A
. . . A . .Consensus: AGTTTGA TTAA GGCAGC
I want to replace "TTAA" as "NNNN" and let consensus sequence output as
"AGTTTGA NNNN GGCAGC".
How can I do this with samtools/bcftools?
Thanks
David Wang, Nation Taiwan Ocean University
------------------------------------------------------------------------------
BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
