Hi, I am running CNVKIT and I am new to it. I was running a batch on two tumor samples with a flat reference.
anaconda3/bin/cnvkit.py batch 1.bam 2.bam -n -t /refseq_exome_genesymbol_headless_CNVkit.csv -f hg19.fasta --access access-5k-mappable.hg19.bed --output-reference my_flat_reference.cnn -d output -p 6
[E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes
but it still continues to run. Is it because my bam files are not bzipped? could the results still be usable?
Thanks a lot in advance! Eric T.
what is the output of
should be something like "bam version 1" or " gzip compressed data, extra field"
thanks for you answer. It says gzip compressed data, extra field