Asma Riyaz
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Activity overview
Latest activity by Asma Riyaz-
Asma Riyaz commented,
Hello again, Does the following command look alright to you (consider this is the second time I am running the pipeline in order to add samples for joint genotyping), here previous_db is the DB gen...
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Asma Riyaz created a post,
Joint genotyping as cohort size grows
Hello, I am trying to make a workflow for germline variant calling to call SNPs. I start off with aligning (bwa-mem2), variant calling (HaplotypeCaller in gvcf mode) and joint genotyping (Genomics...
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Asma Riyaz commented,
Hello, I tried using the --alleles parameter with a interval list file whose contents below. chr6 154010049 154010049 + rs1319339chr6 154039662 154039662 + ...
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Asma Riyaz commented,
Hello again, Following is an example of few snps targets that I want to focus on while calling variants. chr6 154010049 T,Cchr6 154039662 A,Gchr6 154087567 G,A
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Asma Riyaz commented,
Hello, I understand the -L option is for interval list file. This provides a means to look at specific regions, however my question is can I use a certain targets file as well (this is similar to t...
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Asma Riyaz created a post,
Can I specify a targets file with Haplotypecaller?
I want to provide a target file (similar to -T option in bcftools call) along with the interval list file in GATK. Is there a way in GATK to do the same? Currently I am using mpileup and call to do...
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Asma Riyaz commented,
Bob Handsaker Despite the tool generating an error, it gave an output. Does the tool tend to ignore these variants and generate output based on the rest?
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Asma Riyaz commented,
Here is the VCF file (This is a google drive link). The SV caller I used, called 125905998 as a break end, does GenomeSTRiP not like break ends?
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Asma Riyaz commented,
Bhanu Gandham Thank you Bhanu for connecting me to Bob. Could you kindly let me know why was the other question deleted? Though both questions are on GenomeSTRiP ReciprocalOverlapAnnotator, both th...
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Asma Riyaz created a post,
GenomeSTRiP ReciprocalOverlapAnnotator Annotation track not sorted
While using ReciprocalOverlapAnnotator like so: java -Xmx4g org.broadinstitute.sv.main.SVAnnotator \ -A ReciprocalOverlap \ -R hg38.fa \ -vcf Structural_variant_analysis/FAM1_MU006/cute...