question with call cnv for array data

[lizhan96]

hi there,

I have successfully run the phase pipeline.

but it's seem that the Chromosomal alterations pipeline guileline was only described for the WGS data but not array data? Could you send me some example as reference.

[freeseek]

You can find an array example to download here. MoChA will happily run both on VCFs from WGS or from array data. The output format is almost identical. Do notice though that running on WGS data requires significantly more QC and call filtering efforts.

[lizhan96]

Dose the batch file is required? I don't have such file.

[freeseek]

The batch file is only needed if you are running MoChA through the WDL pipeline. I assume you are running MoChA manually though, so the batch file would not be required. The batch file would be something that the user needs to manually edit when using the MoChA WDL.

[lizhan96]

So could you give me reference code for using MoChA with array data?

I can't find that in the link https://github.com/freeseek/mocha/tree/master/wdl#illumina-example you gave me

[freeseek]

The instructions provided related to data preparation explain to great depth how to input array data.

[lizhan96]

bcftools +mocha \ --genome $assembly \ --input-stats $tsv \ --no-version \ --output - \ --output-type b \ --variants ^$dir/$pfx.xcl.bcf \ --calls $dir/$pfx.calls.tsv \ --stats $dir/$pfx.stats.tsv \ --ucsc-bed $dir/$pfx.ucsc.bed \ --cnp $cnp \ --mhc $mhc_reg \ --kir $kir_reg \ $dir/$pfx.bcf | \ tee $dir/$pfx.as.bcf | \ bcftools index --force --output $dir/$pfx.as.bcf.csi

for this code, which paramnent is required with array data in calling CNV?

[freeseek]

I do not understand what you are asking. Each parameter is optional and has an equal effect whether you run MoChA on array data or WGS data.

[lizhan96]

got it.

I have solved the problem. Thanks for your help!