elhb / WGAcomparison

Scripts for the WGA comparison project

#WGAcomparison

##Usage ###Indatafile First you need to create a indata file with the following format:

# sample SAMPLEID_1
# fastq R1_FILE R2_FILE
# sample SAMPLEID_2
# fastq R1_FILE R2_FILE
...
# sample SAMPLEID_n
# fastq R1_FILE R2_FILE

###Mapping To map the data run:

python scripts/mapReads.py indata.txt

Merging mapped bamfiles and do some QC

To merge the bamfiles and calculate HS metrics run:

python scripts/mergeAndQc.py indata.txt

Call variants

Not implemented. ###Create summary Not implemented.