Hi Colin,
Running following command: samtools mpileup -f ref.fasta sorted.bam | less
shows:
--- less output ---
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
(END)
----
Many Thanks
Sami
2014-10-08 12:18 GMT+03:00 Colin Hercus <[email protected]>:
> 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 <[email protected]> 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 <[email protected]>:
>>
>>> 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 <[email protected]> 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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