Hi Sami,
I'm not sure why that wouldn't work. TRy
samtools mpileup -f ref.fasta sorted.bam | less
and see what you get. If that works I'd expect bcf output would work.
Colin
On 8 October 2014 16:32, Sami Pietilä <sami.piet...@gmail.com> wrote:
> Hi Colin,
>
> Thanks for a reply! Novocraft package looks interesting. However, I am not
> quite sure how to use it in this case. I have a bam file containing the
> alignments and a fasta file for the reference sequences. I am not able to
> produce VCF (at least with samtools) because mpileup does not give anything.
>
> Is there a way of using novoutil to generate a consensus sequence(s) from
> bam without having a vcf file?
>
> Many thanks
>
> Sami
>
> 2014-10-08 5:47 GMT+03:00 Colin Hercus <co...@novocraft.com>:
>
>> Hi Sami,
>>
>> You can use novoutil iupac to generate a new consensus sequence from an
>> original fasta and a vcf file. There's options for selecting variant
>> quality and whether to include indel calls. It can also lift over
>> coordinates on a bed file when applying inserts.
>>
>> It's free to use and part of Novoalign download at www.novocraft.com.
>>
>> Kind Regards, Colin
>>
>> On 7 October 2014 21:22, Sami Pietilä <sami.piet...@gmail.com> wrote:
>>
>>> Hi,
>>>
>>> I haven't been able to create a consensus sequence with samtools. I have
>>> a ref.fasta containing just one sequence and then sorted.bam containing
>>> alignments against the reference.
>>>
>>> "samtools mpileup -uf ref.fasta sorted.bam | bcftools view -cg -" gives
>>> nothing after "#CHROM POS ID REF.." line.
>>>
>>> IGV is able to give the consensus sequence (see below).
>>>
>>> Is there a way to get a consensus sequence using samtools?
>>>
>>> Thanks
>>>
>>> /Sami
>>>
>>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>>
>>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>>
>>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>>
>>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>>
>>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCACCAGGGC
>>>
>>> GACGATGCGTAGCCGGCCTGAGAGGGTGGACGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTA
>>>
>>> GGGAATTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>>
>>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>>
>>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>>
>>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>>
>>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>>
>>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>>
>>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAATAAGTATCCCGCCTGGGGAGTACGG
>>>
>>> CCGCAAGGYTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGYATGTGGTTTAATTCGAMGCAACGCGAAGAA
>>>
>>> CCTTACCAGGTCTTGACATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>>
>>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>>
>>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>>
>>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>>
>>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>>
>>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>> NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
>>>
>>>
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>>>
>>
>
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Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
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