Does the GE Pipeline go through QC checks initially? Can anything cause the pipeline to fail during the initial stages?

The pipeline does not have a QC module. Th reasons due to which the pipeline can fail in the initial stages are given below:

1. The pipeline can fail due to corrupted FASTQ files.
2. The pipeline can fail if the read count in R1 do not match to that in R2.
3. The pipeline can fail in the genotyping step if the contigs/chromosomes in panel are not present in the genome.