Alva ✭✭
About
- Username
- Alva
- Location
- Switzerland
- Joined
- Visits
- 145
- Last Active
- Roles
- Member
- Points
- 51
- Badges
- 8
- Location
- Switzerland
- Full Name
- alva james
Reactions
Comments
-
Hello @Tiffany_at_Broad , Thanks for the reply! The case is, I have 22 chromosome in vcf file. I have a 1814 contigs in reference genome. I need to operate over all 22 chr within vcf as I have no specific list as input or we are not specifically…
-
Hello @Geraldine_VdAuwera @Sheila , I have a question regarding using GenomicsDBImport over CombineGVCFs, I have been using CombineGVCFs for joining 320 gvf files using following memory options, • --java-options '-Xmx350G -XX:+UseParallelGC -XX…
-
@SkyWarrior , I have 1841 contigs or choromosmes in my reference genome including viral sequnces from different types. Hence, I am woundering what would be the interval value. I saw in in someother thread more 100 for --intervals is not recomemmned.
-
@SkyWarrior Thank you! Using GenomicsDBImport is better solution than using Combine gvcfs in this case?
-
Hello My bamout file is empty anyhow I am attaching the IGV screenshot for position VCF file , > > > > #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR NORMAL> > > > 1 14748 . G C . alt_allele_in_…
-
Thank you @Shlee for the explanation. Now I have results from MuTect2 I see all the variants (from 40 patient with the corresponding matching sample as Normal or control) have germline_risk and multi_event_alt_allele_in_normal as clustered events. …
-
@Shlee. Thank you for your reply. So now I started with MuTect2 from GATK and I have a completely different result.Also, it is taking more tan 20 hours to finish one sample. The command line I used is from here, java -jar GenomeAnalysisTK.jar \…
-
Actually, I started using Mutect tools from http://archive.broadinstitute.org/cancer/cga/mutect_run after following all pre-workflow from GATK best practices to find Somatic mutations. Then we used our filtered set of confident somatic mutations fo…
-
@Sheila , @Geraldine_VdAuwera Now I have Vcf files from MuTect2, my samples are RNA-seq and when compared to the number of variants from VARSCAN/GATK --haplotype caller I got really lesser number of variants using Mutect2 on the same samples. That…
-
@Sheila yes :smile:
-
@Geraldine_VdAuwera , Thank you so much..Indexing helped :smile:
-
@shelia, @Geraldine_VdAuwera , So i have added the sample names as tumor and normal in SM of BAM files, and then tried the above command line, but its throwing another error message, ERROR MESSAGE: SAM/BAM/CRAM file . Error details: Reference inde…
-
@Shelia, Thank you
-
(Quote)
-
No its SM:sample for both samples ...
-
@Geraldine_VdAuwera : the actual command line I used, java -jar GenomeAnalysisTK.jar -T MuTect2 --filter_reads_with_N_cigar -R /human_genome37_gatk.fa -I:tumor /BM_ID bam -I:normal BM_CR.bam --dbsnp dbsnp_138_chradded.vcf -o BM_P5_id_cr_Mutect.vc…
-
@Sheila Thanks Shelia, I have another question regarding Mutect2 output file..Could you please take a look ito that..
-
@Geraldine_VdAuwera , I have tried for my RNA-seq samples foloowing teh best pratices guliline.. And here is how output VCf looks like.. chrY 10036237 . A C . alt_allele_in_normal ECNT=1;HCNT=11;MAX_ED=.;MIN_ED=.;NLOD=8.64;TLOD…
-
Ok, Thank you
-
@Geraldine_VdAuwera :Mine is RNA-seq data , and does it applies for that kind of data ??
-
@egeulgen : Could you please share the command line here where you used Tumor and matching Normal samples to get the Somatic mutations using GATK variant finding tool. I want to use the same for my RNA-seq data. Thank you /A
-
Ok, so here GT:AD:DP:GQ:PL 1/1:0,342:342:99:14410,1029,0 So here it is 342/342 is Variant Allele frequency rite..?
-
Each sample
-
yeah I tried, with GF option and now I have the output file, but I have hard time understanding what is QUAL and AC columns means how one can infer Empirical Variant Allele frequency from these information .? the command line I used successfully, j…
-
Or putting the question in another way I ahve AD as GT:AD:DP:GQ:PL 1/1:2,366:368:99:14774,1067,0 in the column And for VAF teh formulate is variant reads / total reads and my question is which is variant read and which is ref read
-
Ok, so i used the flowing command line , java-1.7 -jar -Xincgc -Xmx1586M GenomeAnalysisTK-3.2-2.jar -R /human_genome37_gatk.fa -T VariantsToTable -V sample.vcf -F CHROM -F POS -F ID -F QUAL -F AD -o sample.table to retrieve the field.. But its thr…
-
Hello Shelia, Thank you for your time.. But the issue is the Unmapped reads in my BAM files... Thats why the SPLITNCIGAR was complaing ...Now I could get rid of it by adding -rf Unmappedreads in command line. Like this, /java-1.7 -jar -Xincgc -X…
-
Ok, yeah I have fixed the error, I mean when I indexed the same BAM file and then did a validatesamFile check on it and so it gave me the current output as NO errors Can you post the .dict file? I am sorry i dont see such a file in my directory.. …
-
Hello All, I have tried validatesamfile with the following command /opt/husar/bin/java-1.7 -jar -Xincgc -Xmx1586M /nfs/gcg/husar.gcg10.2-centos-husar3/ngs/java/picard-tools-1.78/ValidateSamFile.jar I=BM_ID_reorder.bam MODE=SUMMARY and it gives me…
-
Hello Sheila, Thank you so much for your reply.! Yes I tried both reorderSam, and validatesamfile /opt/husar/bin/java-1.7 -jar /ReorderSam.jar I=BM_ID_dedupped.bam R=/human_genome37_gatk.fa O=BM_ID_reorder.bam and on that BAM file I have ran valid…