Hi Colin,
Building a consensus sequence with a reference having one sequence seems to
work (with -A). Nice. =)
My true reference fasta has multiple sequences. Is there some additional
parameter for samtools which is needed to make building the consensus
sequences work when having multiple ref references in the ref.fasta? For
some consensus sequences, they can be made if ref contains only one seq but
they are not present when ref contains multiple sequences. IGV seems to be
able to find the consensus seqs in all cases.
Many Thanks
Sami
2014-10-08 16:19 GMT+03:00 Colin Hercus <[email protected]>:
> Hi Sami,
>
> Add the option -A to samtools mpileup
>
> -A count anomalous read pairs
>
> IT seems none of your reads aligned as proper pairs.
>
> Colin
>
>
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