User: haiying.kong

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haiying.kong140
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Posts by haiying.kong

<prev • 95 results • page 1 of 10 • next >
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Comment: C: Somatic Mutation Identification for Tumor without Normal
... Dear Manuel, The website is saying "What genome build is the gnomAD data based on? All data are based on GRCh37/hg19" http://gnomad.broadinstitute.org/faq ...
written 9 hours ago by haiying.kong140
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Comment: C: Somatic Mutation Identification for Tumor without Normal
... Could you please give me complete list of database you use as reference for germline mutations for hg19/hg37? It would be wonderful if you could give me links to download as well :) ...
written 2 days ago by haiying.kong140
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Comment: C: Somatic Mutation Identification for Tumor without Normal
... primary melanoma whole exome sequence. ...
written 2 days ago by haiying.kong140
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Comment: C: Somatic Mutation Identification for Tumor without Normal
... Could you please tell me which database you use as germline mutation list? ...
written 2 days ago by haiying.kong140
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Somatic Mutation Identification for Tumor without Normal
... I have WES for 6 tumors which do not have matching normals. I identified all mutations, both germline and somatic with GATK. Then excluded all mutations that are considered as germline by ExAC, and germline mutations that are identified from our about 90 normal samples. The number of somatic mutatio ...
somatic mutation written 2 days ago by haiying.kong140
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Comment: C: Meerkat for identification of somatic structural variations for paired samples
... I am trying to filter variants by following the recommended steps on the manual. Our data is WES for paired samples of normal and tumor. Average depth is 60. If I run the following commands they all give empty output files without any errors. I checked all input files, and they are correct. Tweaked ...
written 2 days ago by haiying.kong140
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Comment: C: Number of Threads for BWA MEM
... It does not have advantage if the number of thread is 2**N, is this correct? ...
written 7 days ago by haiying.kong140
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Number of Threads for BWA MEM
... Is it recommended to use number of threads for BWA MEM, 2**N (4, 8, 16, 32...)? Or any number is as good as well as long as the memory can support? ...
bwa written 7 days ago by haiying.kong140
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Answer: A: Meerkat for identification of somatic structural variations for paired samples
... I think the rmsk data is: rmsk.txt.gz on the link: http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/ ...
written 7 days ago by haiying.kong140
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Meerkat for identification of somatic structural variations for paired samples
... ************************************************************************************************** Apparently, I did not read through the manual carefully. somatic_sv.pl has some parameters that provide information for normal genome. ***************************************************************** ...
somatic structural variations written 7 days ago by haiying.kong140 • updated 7 days ago by gdavidson0

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