"sequenza" - chromosomes are removed when I run 'sequenza.extract'.

Question

[a01039012387]

Hi.

I'm trying to run a "sequenza", but something is wrong. Before I made a pileup file, the bam file has chromosome 1 - 22 and X, Y but when I run a sequenza.extract, there is only chr1.

test <- sequenza.extract("out_PAAD_small.seqz.gz") Processing chr1: 42 variant calls; 2970 heterozygous positions; 357535 homozygous positions. names(test) [1] "BAF" "ratio" "mutations" "segments" "chromosomes" [6] "gc" "avg.depth" test$chromosomes [1] "chr1"

I don't know what happend. Could anyone let me know how can I get all chrs as an output?

[Fabio Marroni]

What is in the file: out_PAAD_small.seqz.gz? Try and see if all the chromosomes are in the file. I tried sequenza on the test data set and it worked fine, so it is possible that there is a problem with the input.