Convert fastq to plink .bed

Question

[genomics Newbie]

I’m a genomic newbie, so I believe my question is a basic one.

I need to transform raw fastq files into plink .bed files. From my biostar searchers it appears I cannot directly transform fastq sequence files to a .bed format, as I would first need to first transform the fastq to .bam files. It appears after I generate .bam files I can then convert these .bam to plink .bed files?

Questions:

• Which tools (i.e. galaxy, etc) are best to convert fastq to .bam

• Which tools (i.e. bedTools) can be used to convert .bam to plink .bed

Any additional information regarding these format "conversions" would be helpful. I had difficulty installing Bowtie.

Thank you!

[genomics Newbie]

Any information about necessary alignments would also be helpful!

[Pierre Lindenbaum]

good luck with that.

[WouterDeCoster]

I'm sure you can come up with a join/comm/awk oneliner for this conversion.

Answer 1

[WouterDeCoster]

"Converting" fastq to bam is called alignment. You didn't tell us about the data format you have, but if it's just regular DNA sequencing you should be fine with bwa mem.

After alignment, you should do variant calling on the bam to get a vcf file of variants. This could be done using samtools/bcftools or GATK.

The vcf you obtained can then be converted to plink.bed using, well, plink.

[genomics Newbie]

Thank you so very much for your quick response. Yes, you are correct that my original format is just regular DNA sequencing (fastq format).

By bwa mem do you mean Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)? Can i do the alignment with any of the packages in galaxy? I can use the samtools in Galaxy, correct? I will also try the Genome analysis toolkit.

[WouterDeCoster]

I don't use galaxy, but yeah, those tools would be fine.