search

zzhang526 / MosaicHunter

A tool to detect postzygotic single-nucleotide mosaicism from unpaired, trio, or paired samples.
http://mosaichunter.cbi.pku.edu.cn/
MIT License
11 stars 4 forks source link

Ratio NaN% #1

Closed PamelaMehanna closed 6 years ago

PamelaMehanna commented 6 years ago

Hi,

I am trying to use your tool for my WES normal data. I tried running the demo dataset and it worked. But when I try using mine, this is what I get: ############################################ [user@cluster build]$ java -jar mosaichunter.jar -C /path/bin/MosaicHunter/conf/exome_parameters.properties.cd_422 ############################################

MosaicHunter 1.0 Tue Feb 27 14:13:43 EST 2018 Parameters: -C /path/bin/MosaicHunter/conf/exome_parameters.properties.cd_422 ............. *To view all parameters used, see file: log_test_MH.txt .............. Tue Feb 27 14:13:43 EST 2018 Reading reference from file: /path/bin/MosaicHunter/resources/human_g1k_v37.fasta Tue Feb 27 14:14:33 EST 2018 Initializing filters... Tue Feb 27 14:14:36 EST 2018 Scanning... Tue Feb 27 14:14:36 EST 2018 - Time(s):0 Reads:0 Sites:0/3095677412 Progress:0.00% Tue Feb 27 14:14:36 EST 2018 - Time(s):0 Reads:0 Sites:3095677412/3095677412 Progress:100.00% filter name pass/all ratio depth_filter 0/0 NaN% base_number_filter 0/0 NaN% repetitive_region_filter 0/0 NaN% homopolymers_filter 0/0 NaN% indel_region_filter 0/0 NaN% heterozygous_filter 0/0 NaN% strand_bias_filter 0/0 NaN% within_read_position_filter 0/0 NaN% complete_linkage_filter 0/0 NaN% exome_parameter_filter 0/0 NaN% null_filter 0/0 NaN% No data. ############################################

For info, Blat is installed as well as the latest Java. I don't understand why it can't read any sites.. My initial .bam file works in other analysis so I don't think the problem lies there.. though I should note that the chromosomes in the .bam are annotated chr1 and not 1.. could that play in the issue? I tried using a reference file with the same annotation but the problem remains.

Thank you for your help!

AugustHuang commented 6 years ago

Yes. The issue is caused by the inconsistent chromosome names. You might want to change the parameter "valid_references" to the chromosome names in your bam. Please note that all the required bed files provided in the "resources" folder were based on GRCh37 with chromosome names 1, 2, ..., so you also need to liftover or generate new bed files which have the same chromosome names as your input bam and reference fasta files.

PamelaMehanna commented 6 years ago

Thanks, it worked.