Hi Sami,
I'm not sure about that. Also I'm not sure if mpileup consensus will
include indel corrections.
Kind Regards, Colin
On 9 October 2014 19:17, Sami Pietilä <[email protected]> wrote:
> 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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