Running pileup_and_phase.R on Parse bam files

[Zgautier]

Hello,

I am trying to run Numbat on bam files coming from a Parse single cell experiment and not a 10X one.
I first tried with a 10X file to make sure everything works and it ran normally. Then, I just changed the bam file and the barcodes file, and I have an error in the pileup_and_phase.R script. I think that the bam file format is the problem.

Here is a read from the 10X bam file for which it ran fine :
A00729:476:HN3TWDSX5:1:1310:32669:1297 16 chr1 10012 1 42M23N48M * 0 0 CTTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCTAACCCTAACC FFFFFF,FFFFFFFFF,FF:FFFFFFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NH:i:3 HI:i:1 AS:i:84 nM:i:2 RG:Z:CHC3115N:0:1:HN3TWDSX5:1 RE:A:I xf:i:0 CR:Z:CTAACCCTAACCCTAA CY:Z:FFFFFFFFFFFFFFFF CB:Z:CTAACCCCAACCCTAA-1 UR:Z:CCCTTAACCCTT UY:Z:FFFFFFFFFFFF UB:Z:CCCTTAACCCTT

And here is a read from the Parse bam file for which it did not work :
23_14_08__R__119_14_8__CTTCTGTA_AACCGAGA_CATCAAGT__GTTCAAAAAG__241027RV_NAGATCAC+NTGTGAAG 16 chr1 8873480 255 20S131M * 0 0 CAACCACCTCCTTCTGTATTGTCTTTTGTTGCTTAAAGTTCATTAATATCCAAGTAGAAAGTTCCACCCATTGACTAAGCAAACCACTCTTACTGGATGAAGGGAATTCTTGGCATCCTGTGAGAACCCTCAGGGTTCCCCATAAAGCCAG III9IIIIIIIII-I-I9IIIIII-IIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9III-I-III9IIII9IIIIIII9III9IIIIII-IIIIIIIIIIIII9III9-IIIIIIIIIII99II NH:i:1 HI:i:1 AS:i:129 nM:i:0 GX:Z:ENSG00000074800 GN:Z:ENO1 pN:Z:GTTCAAAAAG CR:Z:CTTCTGTA_AACCGAGA_CATCAAGT pB:Z:119_14_8pS:Z:ech_5 RE:Z:I RG:Z:parse_chr_sorted_Librairie_1 CB:Z:23_14_08__s1

You will find attached the error log file and the output file (I subsetted the bam file for just one cell so it would be quicker).
Thank you in advance,

Zoé

pileup.log
test_error_numbat.log
test_output_numbat.log