error running pipeline_qc_copynumbercalls()

[chelauk]

Hi

I am running some whole genome analysis but I am getting the attached error

using mutect2 and sequenza

run this
fit <- pipeline_qc_copynumbercalls( mutations = snv_marked, cna = cna_calls, purity = 0.99, smooth = TRUE, reference = "GRCh38", description = "PANORAMA_022_R1T2", ccf_method = "ROUGH", peak_method = "closest", purity_error = 0.03 )
error_output.txt

any help ideas appreciated

[caravagn]

Mmmm looks like some error possibly when looking at 2:2 mutations. Since I see

2:2 [n = 5, L = 2 Mb]

are they just too few mutations? Can you double check that the erorr is gone if you drop that segment?

[chelauk]

Mmmm looks like some error possibly when looking at 2:2 mutations. Since I see

2:2 [n = 5, L = 2 Mb]

are they just too few mutations? Can you double check that the erorr is gone if you drop that segment?

I get a similar error after removing that segment...

cna_qcerr2.txt

[chelauk]

fit <- pipeline_qc_copynumbercalls(
mutations = snv_marked,
cna = cna_calls,
purity = 0.99,
smooth = TRUE,
reference = "GRCh38",
description = "PANORAMA_022_R1T2",
ccf_method = "ROUGH",
peak_method = "closest",
purity_error = 0.03
)
snv_marked.csv.gz
cna_calls.csv