Simple SNP calling pipeline in Linux

[@sinumolgeorge9681]

Thank you for the neat and precise explanation

[@KevinT]

Thank you for this video! It was really helpful.

[@leogaspar8529]

thank you. clear and concise step by step. Nice!

[@rupalhatkar4695]

Could you please make a video on how to call germline SNV,CNVs, and SVs using GATK4? Thank you!!

[@pharmacyseries8178]

can any one help the vcf file appear but without a header only metadata why this is occur

[@princy6425]

Hey, Thank you it was very helpful. 😀

[@KountayDwivedi]

Hi, Thank you for this amazing tutorial. I have a doubt and I need your clarification: I have a reference genome file (hg38.fasta) and a sample single read file (demo.bam). How am I suppose to proceed with mapping step with these files in hand? I am unable to use mem command with .bam file. Thanks. :-}

[@jacobi_official8590]

Hey, just to contribute, if your single read file is in bam format, you can convert bam to fasta then use wba to map this to ref genome.

[@KountayDwivedi]

@@jacobi_official8590 Thanks Peters. However, if we are converting bam to fasta, won't there be a loss of certain information? Or, is there a tool that could do this task losslessly?

[@jacobi_official8590]

@@KountayDwivedi You definitely will not get all info like you would in a fastq file. But I have done it a couple of times. use the bam2fq tool (samtools). You can also see the manual (samtools bam2fq) to see what options to include.

[@sreekaranireddy985]

Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid [E::bcf_hdr_read] Invalid BCF2 magic string: only BCFv2.2 is supported Failed to open seq5.bcf: could not parse header I am getting error like this. Which version you used for this SNP calling? Please kindly give a reply.

[@zvxcvxcz]

You probably need whatever version is specified in the bcf header. I think the latest versioned release per se is 1.9, I would recommend using that. This is written on 05/29/2020 and this advice will lose relevance over time.

[@pramitthapa283]

Thanks for the video. Suggestion: Clearly speak out all the words. Speaking at very low volume towards the end of each sentence doesn’t help us understanding what you are telling

[@congtranxuan1747]

PerA.fa where ??