robertzeibich

testrun for region chr1:1000-2000 takes ages

2

I just wanted to try mosdepth on some of my smaller deletions: `mosdepth --by

TRUTH.TOTAL differs despite having used the same TRUTH SET

2

Do you know why the TRUTH.TOTAL differs despite having used the same TRUTH SET?

When I run hap.py with an already reduced TRUTH_VCF and QUERY_VCF, I get the following error: ``` python /projects/xm41/tools/hap/hap.py-build/bin/hap.py joint.gatk.vqsr.pass.FORMATrm.chr12:20723743-20766328.vcf.gz joint.deepv.FORMATrm.chr12:20723743-2076 6328.vcf.gz -f /projects/xm41/robert/compDeepVGATK/HG001_GRCh38_1_22_v4.2.1_benchmark_HC.bed.gz -r /scratch/xm41/hg38_resources/resources_broad_hg38_v0_Homo_ sapiens_assembly38.fasta -o chr12.19061524-21472881.FORMATrm.GATKts_DEEPV [I]...

manta version: /manta/1.5.0 Why is START and END the same? chr1 3260742 MantaINS:2:652:652:0:3:0 A 999 PASS END=3260742;SVTYPE=INS;CIPOS=0,5;CIEND=0,5;HOMLEN=5;HOMSEQ=TGATG;LEFT_SVINSSE Q=TGATGGTGATGATAATGATAGTGATGGTGATGATGATGGTGGTGGTGATGGTGATGGTGATGGTGGTGGTGATGATGGTGATGGTGATGATGGTGGTGGTGATGATGGTGGTGGTGATGATGGTGATGGTGATGATGGTGATGGTGGTGATGATG GTGGTGG;RIGHT_SVINSSEQ=GGTGGTGATGATGGTGATGGTGGTGATGATGATGGTGATGATGGTGATGGTGATGATGGTGATAATGATAGTGGTGATGATGGTGATGATGATAGTGATGATGATGGTGATGATGGTGATGGCGGCGATGATGG TGATGATGATGGTGATGGTTGTGATGATGTTGGTGATGGTGGTGATGATGATGGCATGATGGCAGTGATTCAAG GT:FT:GQ:PL:PR:SR 1/1:PASS:105:999,108,0:0,14:0,24 What is the length of the insertion? I...

Could you please tell me what I can derive from the files in the stats folder? Why do I want to look at these statistics? I am also curious where...

Why REF = N?

1

Do you know why for the REF N is displayed? Is there also a way to obtain the ALT sequence? #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT GALF003...

When I use smoove annotate, I just receive a MSHQ/SHQ of -1

12

using smoove 0.2.7 GFF="Homo_sapiens.GRCh38.105.gff3.gz" # http://ftp.ensembl.org/pub/release-105/gff3/homo_sapiens/Homo_sapiens.GRCh38.105.gff3.gz smoove annotate --gff ${GFF} ${outdir}/${SAMPLE}.vcf.gz | bgzip -c > ${outdir}/${SAMPLE}.annotated.vcf.gz" Do you know why I just receive for MSHQ/SHQ -1? I am just using...

bcftools differs in depth from IGV and samtools

3

I would like to evaluate the performance of different variant callers based on the BAM file. I tried samtools, but with samtools, I do not get information on strand bias,...

Cutoff for duplications

6

The cutoff for deletions is DHFFC 0.7. What is the recommended DHBFC cutoff for duplications?

Should the tool duphold also work on small deletions <50bp?

4

I got 12 true positive deletions with deletion sizes from 1 to 16bp. However, only for the deletion with a size of 16, I got a DHFFC < 0.7. Seems...