User: vaish01kv

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vaish01kv0
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Posts by vaish01kv

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Comment: C: Bam to mapped fasta
... Thank you so much.. I got it! ...
written 7 days ago by vaish01kv0
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Comment: C: Bam to mapped fasta
... @RG ID:SampleName_S1_L005_001_1 PL:ILLUMINA PU:SampleName_S1_L005_001_1 LB:SampleName_S1_L005_001 SM:SampleName_S1_L005_001 @PG ID:bwa CL:/usr/local/sentieon-genomics-201808/libexec/bwa mem -t 32 genome/hs38DH.fa /home/dnanexus/in/reads_fastqgzs/0/SampleName_S1_L005_R1_001.fastq.gz /home/dna ...
written 9 days ago by vaish01kv0
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Comment: C: Bam to mapped fasta
... �BC]'�]M�6�Qv�Oa�l�?g�D@��P �Q�D )B�����m�U����w7���q���q\��ɏ��/�����}�w���/�������|��?��O���?����?�/�ǃ��K����Aj�b�ǃ�<�L�=h�R�����������Vz��$���|޿ %����o�#�H��'��T�x���η�}�},@s������R��� P����/> ��K�|a��������&|�~�ŵV�����k��E~�)���������� ...
written 9 days ago by vaish01kv0
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Comment: C: Bam to mapped fasta
... I'm not provided with the used reference fasta file. Is there any way i could extract it from BAM file which was provided to me? ...
written 10 days ago by vaish01kv0
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AnnotSV, Ranking, empty ranking column
... I get an empty "AnnotSV ranking" column in the result file. Can anyone please help me resolve this? TIA ...
annotation next-gen written 10 days ago by vaish01kv0 • updated 5 days ago by Biostar ♦♦ 20
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Comment: C: gatk-launch file missing
... I tried running PreprocessIntervals command: gatk PreprocessIntervals \ -R hg38.fa \ -L file.bed \ -- padding 0 \ -O preprocessed.interval_list and the error I get is A USER ERROR has occurred: Invalid argument ' -R'. How should I work further? TIA ...
written 14 days ago by vaish01kv0
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Comment: C: gatk-launch file missing
... Thanks Wouter. I edited my syntax with `"-Xmx4G"` I still get the same error. ...
written 14 days ago by vaish01kv0
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Comment: C: gatk-launch file missing
... Hi, I get the same error. The command I have given is gatk --java-options "Xmx4G" ConvertBedToTargetFile --input targets.bed --output targets.tsv and the below error shows up A USER ERROR has occurred: 'ConvertBedToTargetFile' is not a valid command. Set the system property GATK_ST ...
written 14 days ago by vaish01kv0
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Comment: C: VisualMSI for MSI Calculation using NGS/WXS
... Hi, README.md file clearly says "higher the EMD, more chances of MSI locus to be instable", and EMD is evaluated against a normal sample. Then how does the algorithm work for case-only mode? Could anyone just explain this? TIA ...
written 15 days ago by vaish01kv0
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MANTA for Structural Variants
... Hi, I need to identify structural variants using MANTA. But I heard that structural variants can be best identified from a 300X exome data and I also read that SVs can be identified from 100x exome data. If latter is the case, how reliable is MANTA for identifying SVs from 100X data? TIA ...
next-gen sequencing written 17 days ago by vaish01kv0

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