Merge all samples to a single file - chr22

sinanshi / ge

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Merge all samples to a single file - chr22 #2

Closed sinanshi closed 5 years ago

sinanshi commented 6 years ago

Subsetting issues

There is a large number of VCF outputs are empty - size: 203Kb. My first guess is there are some error occured. Second guess is the chr22 instead of 22 issue.

[x] pick up an empty file and redo the subsetting.
[x] make a script for chr22 style files.
[ ] check empty files, du * | grep K

sinanshi commented 6 years ago

Merge issues

bcftools merge -0 *.vcf.gz > merged_chr22.vcf.gz AF1000G does not have the same length.

sinanshi commented 6 years ago

Remove duplicates

[ ] rare disease samples have duplicates too. see LP3000174-DNA_F06 It is also causing trouble in the subsetting process that it produces an empty file.
[ ] figure out which sample to take from cancer cohort.