Gabriel Renaud comments

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                                            Gabriel Renaud

vcf to G-phocs

Hi Glaucia, thank you for your interest in our software! Yes you should be able to. Just convert your multi sample VCF to ACF and then export to gphocs. Let...

deamSim terminated successfuly but 0 sequences were written

you need to put a bam file, you put `[path to my BAM file]`

deamSim terminated successfuly but 0 sequences were written

`./deamSim -mapdamage ../examplesMapDamage/results_Ust_Ishim/misincorporation.txt single -b

deamSim terminated successfuly but 0 sequences were written

Ok just to be sure, these are not aligned fragments correct? deamSim is for unaligned sequences that need to be realigned.

deamSim terminated successfuly but 0 sequences were written

Two ways to go about this: 1) create an unaligned bam file stripped of all mapping information 2) transferring them to fastq and fastq to bam. You can even do...

deamSim terminated successfuly but 0 sequences were written

reread my point 2, you missed converting back to bam.

deamSim terminated successfuly but 0 sequences were written

samtools import does not really exist anymore, can you update samtools?

deamSim terminated successfuly but 0 sequences were written

I see! I got: samtools import [main] "samtools import" has been removed. Please use "samtools view" instead. This is weird, can you email me the first 100 records of your...

deamSim terminated successfuly but 0 sequences were written

please send it via email, not github.

deamSim terminated successfuly but 0 sequences were written

I see now these are paired-end sequences, not single end. So I did the following, I just considered the forward reads. otherwise, the assumption of independence between fragments is gone....