About hg38 reference genome indexing

Question

[kwanghoon]

Hi

I tried to index reference genome fasta (hg38) that I downloaded UCSC version from below https://www.gungorbudak.com/blog/2018/05/16/how-to-download-hg38-grch38-fasta-human-reference-genome/

Used bwa, samtools(.fa.fai), picard(.dict)

Commands are

bwa index -a bwtsw hg38.fa

samtools faidx hg38.fa

java -Xmx2048m -jar path/to/picard.jar CreateSequenceDictionary -R hg38.fa -O hg38.dict

I found some weird chromosomes like these

1. @SQ SN:chr17_KI270729v1_random LN:280839
2. @SQ SN:chr1_KI270706v1_random LN:175055

Is this normal? or I did something wrong?

Answer 1

[GenoMax]

See: A: Should I keep up with random contigs in human genome

[kwanghoon]

Thank you now I can understand..!