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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