zzq
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Activity overview
Latest activity by zzq-
zzq commented,
Dear all, Here is the comments from Bob, it works for me when setting "-memLimit 8". Hi, One approach is to pass -memLimit N (gigabyte units, e.g. -memLimit 4), which will set the default java memo...
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zzq created a post,
change the memory when running SVPreprocess
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: b) Exact command used: mx="-Xmx200g"ms="-Xms40g"java -cp ${classpath} ${ms} ${mx} -jar ${SV_DIR}/lib/SVToolkit.jar# Run ...
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zzq commented,
Dear Bob Handsaker Thank you for your promtely reply. My samples are not a homogeneous population as they were collected from wordwide and also contain the wild species. I have done PCA based on wh...
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zzq created a post,
run GenerateHaploidCNVGenotypes without population information
Dear Bob Handsaker Version SVToolkit version 2.00 (build 1982)Build date: 2020/08/05 21:29:02 I ran `GenerateHaploidCNVGenotypes` successfully, but with a warning "No population map specified: assu...
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zzq commented,
Dear Bob Handsaker The log file is as follows: INFO 01:16:22,554 HelpFormatter - --------------------------------------------------------- INFO 01:16:22,557 HelpFormatter - Program Name: org.broadi...
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zzq commented,
Dear Bob Handsaker Thank you. The X and Y chromosomes are included in -L, the content of -ploidyMapFile is as following, in which I removed the PAR region from X and Y. X 1 1029481 F 2X 1 1029481 M...
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zzq commented,
dear Bob Handsaker I ran preprocessing for each sample with "-L chr.list" parameter, here all the autosomes and sex chromosomes are included in the chr.list file. Do you mean that preprocessing wil...
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zzq commented,
Dear Bob Handsaker Thank you. The autosomes, X and Y chromosomes are all included in the chr.list, why SVpreprocess can not predict the gender information of the sample. 1:1-end2:1-end3:1-end4:1-e...
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zzq created a post,
sample_gender.report.txt is empty when running SVpreprocess restricted to chromosomes
Dear Bob Handsaker When running SVpreprocess for each sample, I used the option "-L chr.list" to exclude many jobs on scaffolds, as the number of scaffolds is greater than the number of chromosomes...
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zzq commented,
Dear Bob Handsaker I know why program failed when genotyping, as the bam file was not included in the process of SVPreprocess. Sincerely, Zheng Zhuqing