Pirates GM Ben Cherington has big decision on which prospects to protect from Rule 5 Draft

As the deadline approaches for the Pittsburgh Pirates to protect prospects from the Rule 5 Draft, general manager Ben Cherington finds himself having to make decisions on his own acquisitions.

Per MLB rules, those eligible include players who signed at age 18 or younger must be added to a team’s 40-man roster within five seasons or players who signed at age 19 or older within four seasons. If not, they are risked losing to the Rule 5 Draft.

For the Pirates, that includes six prospects ranked in the top 30 of their farm system by both Baseball America and MLB Pipeline — including former first-round pick Travis Swaggerty — as well as six players Cherington acquired by trade.

While some decisions are no-brainers, the Pirates have to weigh how many minor leaguers they want to carry on their 40-man roster and whether they are willing to lose players received in key trades.

“I would say it’s a factor,” Cherington said late last month. “It’s weighed. It’s not the only factor. I couldn’t give you with precision how much any particular factor is weighed because it’s probably all weighed differently, depending on the player and other pieces of the puzzle.

“If there’s more opportunity at the major league level, for example, then that might weigh in the decision to add a player who plays at the position at the upper level who has more opportunity, or we think has more opportunity. There’s some players who we just know are going to be added and proximity isn’t really a big part of it. In some cases, it is part of the conversation. There’s always more than one thing.”

Some of the decisions are no-brainers. Shortstop Liover Peguero was part of the package from Arizona in the Starling Marte trade in January 2020 and the Pirates’ No. 5 prospect is a definite keeper. The 20-year-old Peguero batted .270 with a .776 OPS, 19 doubles, 14 home runs and 45 RBIs for High-A Greensboro this past summer.

Tahnaj Thomas, a 6-foot-4 right-hander who is a top-15 prospect, also appears to be a long-term piece. Thomas, 22, was 3-3 with a 5.19 ERA, 62 strikeouts and 35 walks in 16 starts for Greensboro.

The 24-year-old Swaggerty, a center fielder who was picked in the first round in 2018, could be the key. After spending the 2020 season at the alternate training site, he was fast-tracked to Triple-A Indianapolis last summer but had season-ending surgery to repair his fractured right (non-throwing) shoulder in June.

Cody Bolton is another former top-10 prospect whose status slipped after season-ending knee surgery, and the Pirates could be willing to risk the 23-year-old right-hander to the Rule 5 Draft.

What Cherington will do with players he picked up over the past year will be telling, given that they were part of the returns in the trades involving Josh Bell, Joe Musgrove, Jameson Taillon and Adam Frazier.

Right-hander Eddy Yean, 20, was acquired from Washington in the Bell trade, and went 5-2 with a 5.27 ERA and 9.3 strikeouts per nine innings in 22 games at Low-A Bradenton.

Lefty Omar Cruz, 22, was part of the return from San Diego in the Musgrove trade. Cruz was 3-3 with a 3.45 ERA in seven starts at Greensboro, then went 3-4 with a 3.44 ERA in 14 starts at Double-A Altoona but saw his strikeout rate dip in the process.

Outfielder Canaan Smith-Njigba, acquired from the New York Yankees in the Taillon trade, hit .274 with an .805 OPS in 66 games with Altoona but went 2 for 21 in seven games with Indianapolis.

Outfielder Jack Suwinski, acquired from the Padres in the Frazier trade, hit 15 homers for Double-A San Antonio but had only four for Altoona. And right-hander Michell Miliano was 2-2 with a 6.30 ERA and had more walks (26) than strikeouts (23) in 16 games for Greensboro.

One of the biggest questions will be what the Pirates do with Mason Martin, their 2019 minor league player of the year. The 22-year-old first baseman hit 22 home runs at Altoona and three in eight games at Indianapolis but batted .241 with 171 strikeouts and only 39 walks in 120 games last season.

The Pirates already trimmed the 40-man roster to 37 by releasing infielder/outfielder Phillip Evans, pitcher Tanner Anderson and catcher Taylor Davis, and will make more moves before Friday. Players at risk of losing their roster spot include pitchers Eric Hanhold, Cody Ponce and Duane Underwood Jr., outfielder Jared Oliva and catcher Michael Perez.

Last year, the Pirates cleared room by designating veterans in outfielder Jose Osuna and pitchers Clay Holmes and Trevor Williams for assignment, as well as a former first-rounder in first baseman Will Craig. Cherington warned after the trade deadline in late July that he was prepared to lose some players or prospects this time.

“If and when teams do lose players in Rule 5, if that happens at any point for a team, they’re mostly teams that have a lot of talent, have a lot of players,” Cherington said. “The more you have, the more likely at some point along the way, you’re going to lose some. We’re just comfortable accepting that the more players we have over time, we’re going to lose some of those players. It’s up to us to make sure we do whatever we can to help players get better while they’re here, to help players be at their best, make good internal evaluations on that. Get the right ones to our major league team so we can win.”