bam2seqz only processes one chromosome

[Giorgia Gandolfi]

Hi,

I am using the command bam2seqz using mpileup format with -p parameter as follows:

sequenza-utils bam2seqz -p -n normal.mpileup -t tumor.mpileup -F {input.ref_fasta} \
             -gc {input.gc} -o {output.seqz}

The final seqz.gz file has only chr11 in the output. Any suggestion?
Thanks

Giorgia

[Davide Cittaro]

Do the two input file have the same chromosome order? I had similar issue recently and realized that chromosomes in tumor were sorted lexicographically (chr1, chr10...) and were natsorted in normal (chr1, chr2…)