search

virajbdeshpande / AmpliconArchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
Other
131 stars 41 forks source link

AA amplicon number：NA #131

Closed jingydz closed 1 year ago

jingydz commented 1 year ago

Hi, I use the AmpliconSuite-pipeline software to call ecDNA using my WGS data.

Command

/Parastor300s_G30S/zhangjj/software/miniconda3/bin/python3 /parastor300/work01/zhangjj/software/AmpliconSuite-pipeline/PrepareAA.py -s 6605D -t 50 --cnvkit_dir /parastor300/work01/zhangjj/software/cnvkit/cnvkit.py --bam 6605D.bam --ref GRCh38 --downsample 10.0 -o 6605D_AA_OUT --run_AA --run_AC

Question

Why did I not get the amplicon related files? Does it not detect an amplicon? image All stages appear to have completed successfully.

jluebeck commented 1 year ago

Hi,

This is a completely normal output - it indicates your sample does not have focal amplifications. I believe this was to be expected as you described in another thread that this sample is a normal sample - and we do not expect focal amplifications in normal samples.

Thanks, Jens