Hi Colin,
Thank you very much for your help! I believe I can manage with the ability
to create one consensus seq at a time.
BR,
Sami
2014-10-09 15:15 GMT+03:00 Colin Hercus <co...@novocraft.com>:
> 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 <sami.piet...@gmail.com> 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 <co...@novocraft.com>:
>>
>>> 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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